Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
PRDM16	63976	broad.mit.edu	37	1	3334561	3334561	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3334561G>A	uc001akf.2	+	11	2941	c.2861G>A	c.(2860-2862)AGG>AAG	p.R954K	PRDM16_uc001akc.2_Missense_Mutation_p.R953K|PRDM16_uc001akd.2_Missense_Mutation_p.R953K|PRDM16_uc001ake.2_Missense_Mutation_p.R954K|PRDM16_uc009vlh.2_Missense_Mutation_p.R654K	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	954	Mediates interaction with SKI and regulation of TGF-beta signaling.|C2H2-type 8.|Interaction with CTBP1 and CTBP2 (By similarity).				brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		TACACGTGCAGGTGAGGGGCC	0.652			T	EVI1	MDS|AML								9	15	---	---	---	---	PASS
SLC25A33	84275	broad.mit.edu	37	1	9613784	9613784	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9613784C>G	uc001apw.2	+	2	380	c.157C>G	c.(157-159)CAG>GAG	p.Q53E	SLC25A33_uc001apx.2_5'UTR	NM_032315	NP_115691	Q9BSK2	S2533_HUMAN	mitochondrial carrier protein MGC4399	53	Helical; Name=2; (Potential).|Solcar 1.				transport	integral to membrane|mitochondrial inner membrane					0	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)		CTACTATCCTCAGGTTCATCT	0.478													17	38	---	---	---	---	PASS
VPS13D	55187	broad.mit.edu	37	1	12409360	12409360	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12409360G>A	uc001atv.2	+	46	9501	c.9360G>A	c.(9358-9360)GTG>GTA	p.V3120V	VPS13D_uc001atw.2_Silent_p.V3095V|VPS13D_uc001atx.2_Silent_p.V2307V	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3119					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CCAATGTAGTGAAGACTGCAG	0.468													30	76	---	---	---	---	PASS
PQLC2	54896	broad.mit.edu	37	1	19652073	19652073	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19652073C>A	uc001bby.2	+	5	731	c.379C>A	c.(379-381)CTG>ATG	p.L127M	PQLC2_uc001bbz.2_Missense_Mutation_p.L62M|PQLC2_uc001bca.2_Missense_Mutation_p.L127M|PQLC2_uc001bcb.2_Missense_Mutation_p.L16M|PQLC2_uc001bcc.2_Missense_Mutation_p.L16M	NM_017765	NP_060235	Q6ZP29	PQLC2_HUMAN	PQ loop repeat containing 2 isoform 1	127	Cytoplasmic (Potential).					integral to membrane					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCGCCCCTCTCTGTGTGAGTA	0.557													5	34	---	---	---	---	PASS
UBXN10	127733	broad.mit.edu	37	1	20517269	20517269	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20517269A>G	uc001bdb.2	+	2	299	c.215A>G	c.(214-216)TAT>TGT	p.Y72C		NM_152376	NP_689589	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	72										ovary(1)	1						GCCATTCCCTATGAGTTGCCA	0.567													27	52	---	---	---	---	PASS
INPP5B	3633	broad.mit.edu	37	1	38344005	38344005	+	Intron	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38344005A>G	uc001ccg.1	-						INPP5B_uc009vvk.1_Intron|INPP5B_uc001ccf.1_Intron|INPP5B_uc010oij.1_RNA	NM_005540	NP_005531	P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ACTGAAATGCAAAGTCCACAC	0.557													13	26	---	---	---	---	PASS
POMGNT1	55624	broad.mit.edu	37	1	46660018	46660018	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46660018G>T	uc001cpe.2	-	9	971	c.807C>A	c.(805-807)TGC>TGA	p.C269*	POMGNT1_uc010olx.1_Nonsense_Mutation_p.C247*|POMGNT1_uc010oly.1_RNA|POMGNT1_uc010olz.1_Nonsense_Mutation_p.C126*|POMGNT1_uc001cpg.2_Nonsense_Mutation_p.C269*|POMGNT1_uc001cpf.2_5'UTR|POMGNT1_uc001cph.1_5'Flank|POMGNT1_uc001cpi.1_5'Flank	NM_017739	NP_060209	Q8WZA1	PMGT1_HUMAN	O-linked mannose	269	Lumenal (Potential).		C -> Y (in MDDGA3; specific activity abolished of the membrane bound form but not the soluble form).		protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					CAACTTTGCTGCAGAAGCGCC	0.602													9	23	---	---	---	---	PASS
BSND	7809	broad.mit.edu	37	1	55474046	55474046	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55474046C>G	uc001cye.2	+	4	951	c.708C>G	c.(706-708)GAC>GAG	p.D236E		NM_057176	NP_476517	Q8WZ55	BSND_HUMAN	barttin	236	Cytoplasmic (Potential).					basolateral plasma membrane|cytoplasm|integral to plasma membrane|protein complex				ovary(1)|skin(1)	2						GCCCGCTGGACCGCTTCCAAG	0.597													6	19	---	---	---	---	PASS
CTH	1491	broad.mit.edu	37	1	70877271	70877271	+	Intron	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70877271G>C	uc001dfd.2	+						CTH_uc009wbl.1_Intron|CTH_uc001dfe.2_Intron|CTH_uc010oqq.1_Intron	NM_001902	NP_001893	P32929	CGL_HUMAN	cystathionase isoform 1						cysteine biosynthetic process|hydrogen sulfide biosynthetic process|protein homotetramerization|protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	cytoplasm|nucleus	cystathionine gamma-lyase activity|L-cysteine desulfhydrase activity|pyridoxal phosphate binding			lung(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)	CACTCGGTGAGCTGGGTCTGT	0.517													8	26	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75037757	75037757	+	Nonsense_Mutation	SNP	C	A	A	rs143506603		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75037757C>A	uc001dgg.2	-	14	3856	c.3637G>T	c.(3637-3639)GAG>TAG	p.E1213*		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1213	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						AAGGCCCCCTCTCCATCTTGG	0.602													21	35	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75038942	75038942	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75038942G>T	uc001dgg.2	-	14	2671	c.2452C>A	c.(2452-2454)CAG>AAG	p.Q818K		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	818	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						AATTCTGGCTGCTCTGCTGTT	0.552													18	67	---	---	---	---	PASS
PIGK	10026	broad.mit.edu	37	1	77620189	77620189	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77620189C>G	uc001dhk.2	-	9	976	c.931G>C	c.(931-933)GAA>CAA	p.E311Q	PIGK_uc010orj.1_Missense_Mutation_p.E235Q|PIGK_uc009wbx.2_Missense_Mutation_p.E217Q|PIGK_uc001dhl.1_Missense_Mutation_p.E311Q	NM_005482	NP_005473	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	311	Lumenal (Potential).|Essential for GPI attachment.			Missing: Loss of activity.	attachment of GPI anchor to protein|C-terminal protein lipidation|protein thiol-disulfide exchange|proteolysis	GPI-anchor transamidase complex	cysteine-type endopeptidase activity|GPI-anchor transamidase activity|protein binding			ovary(2)|pancreas(1)	3						GTTGTAATTTCCACTTTCCGT	0.363													11	25	---	---	---	---	PASS
MCOLN3	55283	broad.mit.edu	37	1	85488037	85488037	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85488037G>T	uc001dkp.2	-	10	1235	c.1142C>A	c.(1141-1143)ACC>AAC	p.T381N	MCOLN3_uc001dko.2_5'UTR|MCOLN3_uc001dkq.2_Missense_Mutation_p.T325N	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3	381	Helical; (Potential).					integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)		CACGAGCATGGTAGAAGTCCC	0.378													15	46	---	---	---	---	PASS
CLCA1	1179	broad.mit.edu	37	1	86959196	86959196	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86959196T>G	uc001dlt.2	+	10	1723	c.1594T>G	c.(1594-1596)TGG>GGG	p.W532G	CLCA1_uc001dls.1_Missense_Mutation_p.W471G	NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor	532					calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		AATCCTTCTCTGGGATCCCAG	0.507													21	48	---	---	---	---	PASS
BARHL2	343472	broad.mit.edu	37	1	91180241	91180241	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91180241C>A	uc001dns.2	-	2	740	c.698G>T	c.(697-699)CGA>CTA	p.R233L		NM_020063	NP_064447	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	233	Homeobox.					nucleus	sequence-specific DNA binding			ovary(1)	1		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		CCTTGCTTTTCGAGGCTTCTT	0.557													39	122	---	---	---	---	PASS
CCDC76	54482	broad.mit.edu	37	1	100598729	100598729	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100598729C>A	uc001dsv.2	+	1	24	c.5C>A	c.(4-6)GCG>GAG	p.A2E	SASS6_uc001dsu.2_5'Flank|SASS6_uc009wdz.2_5'Flank|CCDC76_uc010ouf.1_RNA|CCDC76_uc009wea.2_Missense_Mutation_p.A2E	NM_019083	NP_061956	Q9NUP7	TRM13_HUMAN	coiled-coil domain containing 76	2					tRNA processing		metal ion binding|methyltransferase activity			ovary(1)	1		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0814)|all cancers(265;0.133)|COAD - Colon adenocarcinoma(174;0.146)|Lung(183;0.194)		AGAATTATGGCGACCTCCGCG	0.557													4	32	---	---	---	---	PASS
SORT1	6272	broad.mit.edu	37	1	109910038	109910038	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109910038T>A	uc001dxm.1	-	3	481	c.432A>T	c.(430-432)CTA>CTT	p.L144L	SORT1_uc010ovi.1_Silent_p.L8L|SORT1_uc009wfb.2_Silent_p.L8L	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein	144	Extracellular (Potential).				endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		ACCTTCGATATAGCTTGGACT	0.383													30	100	---	---	---	---	PASS
ATXN7L2	127002	broad.mit.edu	37	1	110028702	110028702	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110028702A>T	uc001dxr.2	+	2	166	c.151A>T	c.(151-153)AAA>TAA	p.K51*	ATXN7L2_uc001dxs.2_5'Flank	NM_153340	NP_699171	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	51										ovary(2)	2		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		GGAGAGTAGCAAAAACACGAA	0.537													20	40	---	---	---	---	PASS
ADAM30	11085	broad.mit.edu	37	1	120437651	120437651	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120437651C>G	uc001eij.2	-	1	1463	c.1309G>C	c.(1309-1311)GCC>CCC	p.A437P		NM_021794	NP_068566	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30 preproprotein	437	Disintegrin.|Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding	p.A437G(1)		ovary(2)|lung(1)	3	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		CTACAGTTGGCACCTGGTTGC	0.453													30	79	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144874717	144874717	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144874717G>C	uc001elw.3	-	30	5182	c.4891C>G	c.(4891-4893)CAC>GAC	p.H1631D	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.H1587D|PDE4DIP_uc001elv.3_Missense_Mutation_p.H638D	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1631	NBPF.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCTTCATAGTGTGTGTACTCG	0.522			T	PDGFRB	MPD								38	216	---	---	---	---	PASS
CGN	57530	broad.mit.edu	37	1	151501956	151501956	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151501956G>T	uc009wmw.2	+	11	2171	c.2027G>T	c.(2026-2028)GGT>GTT	p.G676V		NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin	670	Glu-rich.|Potential.					myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCTGATCGAGGTCGGGAGCTG	0.627													6	31	---	---	---	---	PASS
MEF2D	4209	broad.mit.edu	37	1	156450738	156450738	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156450738C>A	uc001fpc.2	-	4	674	c.284G>T	c.(283-285)GGC>GTC	p.G95V	MEF2D_uc001fpb.2_Missense_Mutation_p.G95V|MEF2D_uc001fpd.2_Missense_Mutation_p.G95V|MEF2D_uc001fpe.1_Missense_Mutation_p.G95V|MEF2D_uc009wsa.2_RNA	NM_005920	NP_005911	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	95					apoptosis|muscle organ development|nervous system development|positive regulation of transcription from RNA polymerase II promoter	nucleus	activating transcription factor binding|histone deacetylase binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GCTGTCGCAGCCGTTGAAGCC	0.667											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	43	---	---	---	---	PASS
APOA1BP	128240	broad.mit.edu	37	1	156563309	156563309	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156563309G>C	uc001fph.2	+	5	665	c.626G>C	c.(625-627)GGA>GCA	p.G209A	APOA1BP_uc001fpg.2_Missense_Mutation_p.G209A|APOA1BP_uc001fpi.2_Silent_p.G190G|APOA1BP_uc001fpj.2_Missense_Mutation_p.G126A|APOA1BP_uc001fpk.2_Missense_Mutation_p.G106A|APOA1BP_uc010php.1_Missense_Mutation_p.G106A	NM_144772	NP_658985	Q8NCW5	AIBP_HUMAN	apolipoprotein A-I binding protein precursor	209	YjeF N-terminal.					extracellular region	protein binding			central_nervous_system(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GTCCTGAAGGGACTCACTGTG	0.567													14	51	---	---	---	---	PASS
INSRR	3645	broad.mit.edu	37	1	156811328	156811328	+	Intron	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156811328C>A	uc010pht.1	-						NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1)	20	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GACCTGGGGGCATGCAGGAGC	0.607													13	39	---	---	---	---	PASS
FCRL3	115352	broad.mit.edu	37	1	157667113	157667113	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157667113C>G	uc001frb.2	-	6	953	c.661G>C	c.(661-663)GAT>CAT	p.D221H	FCRL3_uc001fqx.3_RNA|FCRL3_uc001fqy.3_RNA|FCRL3_uc001fqz.3_Missense_Mutation_p.D221H|FCRL3_uc009wsn.2_Intron|FCRL3_uc009wso.2_RNA|FCRL3_uc001fra.2_5'UTR|FCRL3_uc001frc.1_Missense_Mutation_p.D221H	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	221	Ig-like C2-type 3.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)					AGCTGGACATCTGGCCTCTGT	0.582													25	59	---	---	---	---	PASS
VANGL2	57216	broad.mit.edu	37	1	160395042	160395042	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160395042A>C	uc001fwb.1	+	9	1739	c.1440A>C	c.(1438-1440)TTA>TTC	p.L480F	VANGL2_uc001fwc.1_Missense_Mutation_p.L480F	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2	480	Cytoplasmic (Potential).				apical protein localization|heart looping|nonmotile primary cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTTTCCTCTTAAAACGCCAGG	0.527													20	39	---	---	---	---	PASS
FCGR2B	2213	broad.mit.edu	37	1	161641367	161641367	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161641367G>T	uc001gaz.1	+	3	411	c.319G>T	c.(319-321)GAC>TAC	p.D107Y	FCGR2B_uc009wum.1_Missense_Mutation_p.D107Y|FCGR2B_uc001gay.1_Missense_Mutation_p.D106Y|FCGR2B_uc001gba.1_Missense_Mutation_p.D106Y|FCGR2B_uc001gbb.1_Missense_Mutation_p.D107Y|FCGR2B_uc009wun.1_Missense_Mutation_p.D100Y	NM_004001	NP_003992	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor	107	Ig-like C2-type 1.|Extracellular (Potential).				immune response|interspecies interaction between organisms|regulation of immune response	integral to membrane|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CAACAACAATGACAGCGGGGA	0.587			T	?	ALL								10	33	---	---	---	---	PASS
ADCY10	55811	broad.mit.edu	37	1	167852846	167852846	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167852846C>G	uc001ger.2	-	9	1147	c.849G>C	c.(847-849)CAG>CAC	p.Q283H	ADCY10_uc009wvk.2_Missense_Mutation_p.Q191H|ADCY10_uc010plj.1_Missense_Mutation_p.Q130H|ADCY10_uc009wvl.2_Missense_Mutation_p.Q282H|ADCY10_uc009wvm.2_RNA	NM_018417	NP_060887	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10	283					intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3						ATAAATAGCCCTGAAGCTGTT	0.507													14	41	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176661376	176661376	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176661376C>T	uc001gkz.2	+	6	3710	c.2546C>T	c.(2545-2547)CCA>CTA	p.P849L	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	849					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						ATCCCCATTCCACCTATGGTC	0.517													47	94	---	---	---	---	PASS
UCHL5	51377	broad.mit.edu	37	1	193028549	193028549	+	5'Flank	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193028549C>A	uc001gsm.2	-						UCHL5_uc001gsn.2_5'Flank|UCHL5_uc001gso.2_5'Flank|UCHL5_uc010pov.1_5'Flank|UCHL5_uc001gsp.2_5'Flank|UCHL5_uc001gsq.2_5'Flank|UCHL5_uc010pow.1_Intron|UCHL5_uc010pox.1_5'Flank|UCHL5_uc001gsr.1_3'UTR|TROVE2_uc001gst.1_5'Flank|TROVE2_uc001gss.2_5'Flank|TROVE2_uc001gsu.1_5'Flank|TROVE2_uc001gsv.1_5'Flank|TROVE2_uc001gsw.2_5'Flank|TROVE2_uc009wyp.2_5'Flank|TROVE2_uc009wyq.2_5'Flank	NM_015984	NP_057068	Q9Y5K5	UCHL5_HUMAN	ubiquitin carboxyl-terminal hydrolase L5						DNA recombination|DNA repair|protein deubiquitination|regulation of proteasomal protein catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytosol|Ino80 complex|proteasome complex	endopeptidase inhibitor activity|omega peptidase activity|proteasome binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|ovary(1)	3						TCACCTGCAGCGCGACTGAGC	0.672													3	8	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197071710	197071710	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197071710C>G	uc001gtu.2	-	18	6928	c.6671G>C	c.(6670-6672)TGG>TCG	p.W2224S	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Missense_Mutation_p.W72S	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	2224					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						TTTCATTGCCCAGTATCTTTG	0.328													15	53	---	---	---	---	PASS
CD55	1604	broad.mit.edu	37	1	207510715	207510715	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207510715C>A	uc001hfq.3	+	8	1315	c.1021C>A	c.(1021-1023)CAT>AAT	p.H341N	CD55_uc001hfp.3_Missense_Mutation_p.H341N|CD55_uc001hfr.3_Missense_Mutation_p.H341N|CD55_uc010psf.1_RNA|CD55_uc009xcf.2_Missense_Mutation_p.H277N|CD55_uc009xce.2_Missense_Mutation_p.H341N|CD55_uc009xcg.2_Missense_Mutation_p.H83N	NM_000574	NP_000565	P08174	DAF_HUMAN	decay accelerating factor for complement isoform	341	Ser/Thr-rich.				complement activation, classical pathway|elevation of cytosolic calcium ion concentration|innate immune response|respiratory burst	anchored to membrane|extracellular region|integral to plasma membrane|membrane raft|soluble fraction	receptor activity			ovary(1)	1					Chloramphenicol(DB00446)	CAAGCATTTTCATGAAACAAC	0.423													20	56	---	---	---	---	PASS
CR2	1380	broad.mit.edu	37	1	207644261	207644261	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207644261G>T	uc001hfw.2	+	7	1496	c.1402G>T	c.(1402-1404)GTG>TTG	p.V468L	CR2_uc001hfv.2_Missense_Mutation_p.V468L|CR2_uc009xch.2_Missense_Mutation_p.V468L|CR2_uc009xci.1_5'Flank	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	468	Sushi 7.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						CCAATGCAAAGGTGCCAGGCC	0.443													10	23	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214571303	214571303	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214571303C>G	uc001hkk.1	-	8	982	c.711G>C	c.(709-711)ATG>ATC	p.M237I	PTPN14_uc010pty.1_Missense_Mutation_p.M138I	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type	237	FERM.				lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CGAAAATCCCCATAAAGAAAA	0.289													8	44	---	---	---	---	PASS
BPNT1	10380	broad.mit.edu	37	1	220232316	220232316	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220232316T>C	uc001hma.2	-	9	969	c.797A>G	c.(796-798)CAT>CGT	p.H266R	BPNT1_uc010pug.1_Missense_Mutation_p.H211R|BPNT1_uc010puh.1_Missense_Mutation_p.H230R|BPNT1_uc001hmb.3_Missense_Mutation_p.H281R	NM_006085	NP_006076	O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	266					3'-phosphoadenosine 5'-phosphosulfate metabolic process|nervous system development|xenobiotic metabolic process	cytosol	3'(2'),5'-bisphosphate nucleotidase activity			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0558)		AACATTCCCATGGATATCGGT	0.398													21	50	---	---	---	---	PASS
SLC35F3	148641	broad.mit.edu	37	1	234041399	234041399	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234041399G>C	uc001hvy.1	+	2	323	c.178G>C	c.(178-180)GTG>CTG	p.V60L		NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	Error:Variant_position_missing_in_Q8IY50_after_alignment					transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			GTCGCGCTCCGTGGAGGATCT	0.642													18	43	---	---	---	---	PASS
OR6F1	343169	broad.mit.edu	37	1	247875985	247875985	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247875985G>T	uc001idj.1	-	1	73	c.73C>A	c.(73-75)CTC>ATC	p.L25I		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	25	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			AAGAGAGAGAGCTGAAGAGTT	0.463													16	245	---	---	---	---	PASS
OR14A16	284532	broad.mit.edu	37	1	247978670	247978670	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247978670T>C	uc001idm.1	-	1	362	c.362A>G	c.(361-363)TAT>TGT	p.Y121C		NM_001001966	NP_001001966	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TATAGCAGTATAGCGGTCAAA	0.493													37	111	---	---	---	---	PASS
OR2AK2	391191	broad.mit.edu	37	1	248128902	248128902	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248128902C>A	uc010pzd.1	+	1	269	c.269C>A	c.(268-270)TCC>TAC	p.S90Y	OR2L13_uc001ids.2_Intron	NM_001004491	NP_001004491	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK,	90	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			ATGTACATCTCCACCACAGTG	0.473													30	79	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	248436152	248436152	+	IGR	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248436152G>T								OR2M4 (32987 upstream) : OR2T33 (3 downstream)																							TTTGACATTAGATCATCTTGA	0.388													22	81	---	---	---	---	PASS
OR14C36	127066	broad.mit.edu	37	1	248512845	248512845	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248512845T>C	uc010pzl.1	+	1	769	c.769T>C	c.(769-771)TAC>CAC	p.Y257H		NM_001001918	NP_001001918	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C,	257	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						CTCTTCTGTGTACCTCAGGCC	0.498													24	70	---	---	---	---	PASS
OR14C36	127066	broad.mit.edu	37	1	248512948	248512948	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248512948G>A	uc010pzl.1	+	1	872	c.872G>A	c.(871-873)AGA>AAA	p.R291K		NM_001001918	NP_001001918	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C,	291	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						TACAGTCTTAGAAATAAGCAA	0.413													33	89	---	---	---	---	PASS
OR2T27	403239	broad.mit.edu	37	1	248813460	248813460	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248813460G>A	uc010pzo.1	-	1	726	c.726C>T	c.(724-726)TCC>TCT	p.S242S		NM_001001824	NP_001001824	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T,	242	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCATGTGTGAGGAGCAGGTGG	0.522													6	9	---	---	---	---	PASS
OR14I1	401994	broad.mit.edu	37	1	248845065	248845065	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248845065G>A	uc001ieu.1	-	1	541	c.541C>T	c.(541-543)CAT>TAT	p.H181Y		NM_001004734	NP_001004734	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GCCAACACATGAGGGATGTCA	0.502													16	41	---	---	---	---	PASS
RNASEH1	246243	broad.mit.edu	37	2	3595592	3595592	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3595592C>T	uc002qxt.2	-	7	793	c.703G>A	c.(703-705)GGG>AGG	p.G235R	RNASEH1_uc002qxs.2_Missense_Mutation_p.G118R	NM_002936	NP_002927	O60930	RNH1_HUMAN	ribonuclease H1	235	RNase H.				RNA catabolic process	cytoplasm	magnesium ion binding|ribonuclease H activity|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)		ACCTCTTTCCCTGCACTTGTC	0.448													40	126	---	---	---	---	PASS
CMPK2	129607	broad.mit.edu	37	2	7001358	7001358	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001358C>A	uc002qyo.2	-	3	1058	c.949G>T	c.(949-951)GAA>TAA	p.E317*	CMPK2_uc010yis.1_Nonsense_Mutation_p.E317*|CMPK2_uc010ewv.2_Nonsense_Mutation_p.E317*	NM_207315	NP_997198	Q5EBM0	CMPK2_HUMAN	UMP-CMP kinase 2 precursor	317					dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTAGCTATTTCGGAGGCCACA	0.373													13	51	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21247880	21247880	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21247880G>A	uc002red.2	-	16	2489	c.2361C>T	c.(2359-2361)GCC>GCT	p.A787A		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	787					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	CATGGAGACTGGCAAAACCAA	0.552													22	61	---	---	---	---	PASS
HEATR5B	54497	broad.mit.edu	37	2	37241161	37241161	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37241161T>A	uc002rpp.1	-	27	4203	c.4107A>T	c.(4105-4107)GTA>GTT	p.V1369V	HEATR5B_uc010ezy.1_5'UTR|HEATR5B_uc002rpq.3_5'UTR	NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1369							binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				ATGTACTACATACCTAGACAA	0.333													30	52	---	---	---	---	PASS
HEATR5B	54497	broad.mit.edu	37	2	37265146	37265146	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37265146G>A	uc002rpp.1	-	21	3164	c.3068C>T	c.(3067-3069)ACA>ATA	p.T1023I		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1023							binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				GGAACGAATTGTAGAAGTTGT	0.363													14	42	---	---	---	---	PASS
THADA	63892	broad.mit.edu	37	2	43514126	43514126	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43514126A>G	uc002rsw.3	-	35	5437	c.5085T>C	c.(5083-5085)CCT>CCC	p.P1695P	THADA_uc010far.2_Silent_p.P890P|THADA_uc002rsx.3_Silent_p.P1695P|THADA_uc002rsy.3_RNA	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1695							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TAGACTCTGTAGGAAGATGGT	0.493													31	52	---	---	---	---	PASS
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48873855	48873855	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48873855C>T	uc010yol.1	+	5	2670	c.2623C>T	c.(2623-2625)CTT>TTT	p.L875F	STON1-GTF2A1L_uc002rwp.1_Missense_Mutation_p.L922F|GTF2A1L_uc002rws.1_Missense_Mutation_p.L218F|GTF2A1L_uc010yom.1_Missense_Mutation_p.L184F|GTF2A1L_uc002rwt.2_Missense_Mutation_p.L218F	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	875					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CAGTGATATACTTGTATCTCC	0.413													22	69	---	---	---	---	PASS
SMEK2	57223	broad.mit.edu	37	2	55786013	55786013	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55786013A>G	uc002rzc.2	-	16	2727	c.2352T>C	c.(2350-2352)AAT>AAC	p.N784N	SMEK2_uc002rzb.2_Silent_p.N699N|SMEK2_uc002rzd.2_Silent_p.N752N|SMEK2_uc002ryz.2_Silent_p.N211N|SMEK2_uc002rza.2_Silent_p.N568N	NM_001122964	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 isoform 1	784						microtubule organizing center|nucleus	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TGTTTGTTCCATTAGCAGCAC	0.438													9	186	---	---	---	---	PASS
BCL11A	53335	broad.mit.edu	37	2	60679756	60679756	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60679756T>G	uc010ypj.1	-	4	2554	c.2326A>C	c.(2326-2328)ATG>CTG	p.M776L	BCL11A_uc002sab.2_Missense_Mutation_p.D759A|BCL11A_uc002sac.2_Missense_Mutation_p.M226L|BCL11A_uc010ypi.1_Missense_Mutation_p.D428A	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	Error:Variant_position_missing_in_Q9H165_after_alignment					negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			CTGCCACACATCTTGAGCTCT	0.537			T	IGH@	B-CLL								8	148	---	---	---	---	PASS
B3GNT2	10678	broad.mit.edu	37	2	62449632	62449632	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62449632C>T	uc002sbs.2	+	2	515	c.277C>T	c.(277-279)CTG>TTG	p.L93L		NM_006577	NP_006568	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal	93	Lumenal (Potential).					Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			TATAAGCCATCTGAACTACTG	0.532													160	214	---	---	---	---	PASS
MEIS1	4211	broad.mit.edu	37	2	66662988	66662988	+	5'UTR	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66662988G>C	uc002sdu.2	+	1					MEIS1_uc002sdt.2_5'UTR|MEIS1_uc002sdv.2_5'Flank|MEIS1_uc010yqh.1_5'Flank	NM_002398	NP_002389	O00470	MEIS1_HUMAN	Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0						CAGAGAGGCCGATGGCGCAAA	0.373													4	28	---	---	---	---	PASS
REG1B	5968	broad.mit.edu	37	2	79312409	79312409	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79312409C>A	uc002sny.2	-	6	546	c.434G>T	c.(433-435)GGA>GTA	p.G145V		NM_006507	NP_006498	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta precursor	145	C-type lectin.				cell proliferation	extracellular region	sugar binding			central_nervous_system(1)|skin(1)	2						TTTCTTGAATCCTATGGTACA	0.398													24	21	---	---	---	---	PASS
REG1B	5968	broad.mit.edu	37	2	79312410	79312410	+	Intron	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79312410C>A	uc002sny.2	-							NM_006507	NP_006498	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta precursor						cell proliferation	extracellular region	sugar binding			central_nervous_system(1)|skin(1)	2						TTCTTGAATCCTATGGTACAA	0.393													23	21	---	---	---	---	PASS
ITPRIPL1	150771	broad.mit.edu	37	2	96992653	96992653	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96992653C>T	uc002svx.2	+	3	619	c.284C>T	c.(283-285)CCG>CTG	p.P95L	ITPRIPL1_uc010yuk.1_Missense_Mutation_p.P87L|ITPRIPL1_uc002svy.2_Missense_Mutation_p.P103L|ITPRIPL1_uc010yul.1_Missense_Mutation_p.P87L	NM_001008949	NP_001008949	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-triphosphate receptor interacting	95	Extracellular (Potential).					integral to membrane				central_nervous_system(2)|ovary(1)	3						ATGGGGTGGCCGTTCCAGGCC	0.572													16	32	---	---	---	---	PASS
VWA3B	200403	broad.mit.edu	37	2	98844703	98844703	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98844703G>A	uc002syo.2	+	15	2322	c.2058G>A	c.(2056-2058)CAG>CAA	p.Q686Q	VWA3B_uc002syj.2_RNA|VWA3B_uc002syk.1_RNA|VWA3B_uc002syl.1_Silent_p.Q205Q|VWA3B_uc002sym.2_Silent_p.Q686Q|VWA3B_uc002syn.1_RNA|VWA3B_uc010yvi.1_Silent_p.Q343Q|VWA3B_uc002syp.1_Silent_p.Q78Q|VWA3B_uc002syq.1_Intron|VWA3B_uc002syr.1_Silent_p.Q3Q	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	686										ovary(3)|large_intestine(2)|skin(1)	6						AAATGGAACAGGGTCACAGTG	0.398													19	51	---	---	---	---	PASS
PDCL3	79031	broad.mit.edu	37	2	101185427	101185427	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101185427G>T	uc002tao.2	+	3	280	c.168G>T	c.(166-168)CTG>CTT	p.L56L		NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	56					apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0						TGGAAGAGCTGGAGGATCATG	0.338													20	53	---	---	---	---	PASS
PDCL3	79031	broad.mit.edu	37	2	101185428	101185428	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101185428G>T	uc002tao.2	+	3	281	c.169G>T	c.(169-171)GAG>TAG	p.E57*		NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	57					apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0						GGAAGAGCTGGAGGATCATGA	0.338													19	53	---	---	---	---	PASS
ACTR3	10096	broad.mit.edu	37	2	114699752	114699752	+	Intron	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114699752T>C	uc002tkx.1	+						ACTR3_uc010yyc.1_Intron|ACTR3_uc010yyd.1_Intron	NM_005721	NP_005712	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog						cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding			skin(1)	1						TTTTGTTTCTTTGTTTTTCAG	0.294													10	19	---	---	---	---	PASS
MYO7B	4648	broad.mit.edu	37	2	128346007	128346007	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128346007C>A	uc002top.2	+	15	1784	c.1731C>A	c.(1729-1731)ATC>ATA	p.I577I		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	577	Myosin head-like.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCACAGATATCCTCACCCTGG	0.557													11	21	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141250260	141250260	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141250260C>A	uc002tvj.1	-	57	10009	c.9037G>T	c.(9037-9039)GAA>TAA	p.E3013*		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3013	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AAAGGTTCTTCATCTAAACAC	0.333										TSP Lung(27;0.18)			16	47	---	---	---	---	PASS
MBD5	55777	broad.mit.edu	37	2	149226852	149226852	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149226852G>A	uc002twm.3	+	9	2328	c.1340G>A	c.(1339-1341)GGG>GAG	p.G447E	MBD5_uc010zbs.1_RNA|MBD5_uc010fns.2_Missense_Mutation_p.G447E|MBD5_uc002twn.1_5'Flank	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	447						chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		CACATGATGGGGACTGGAATT	0.507													16	30	---	---	---	---	PASS
TANK	10010	broad.mit.edu	37	2	162036186	162036186	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162036186A>G	uc002ubr.1	+	2	171	c.13A>G	c.(13-15)ATT>GTT	p.I5V	TANK_uc002ubq.1_Missense_Mutation_p.I5V|TANK_uc002ubs.2_Missense_Mutation_p.I5V	NM_004180	NP_004171	Q92844	TANK_HUMAN	TRAF interacting protein TANK isoform a	5						cytosol	metal ion binding|protein binding			ovary(1)	1						GGATAAAAACATTGGCGAGCA	0.393													14	48	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168110642	168110642	+	3'UTR	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168110642G>A	uc002udx.2	+	9					XIRP2_uc010fpn.2_Missense_Mutation_p.C459Y|XIRP2_uc010fpo.2_Missense_Mutation_p.C426Y|XIRP2_uc010fpp.2_Missense_Mutation_p.C426Y|XIRP2_uc010fpq.2_3'UTR|XIRP2_uc010fpr.2_Missense_Mutation_p.C204Y	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CATAAGTCCTGCTTCCGATGC	0.398													11	20	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179425815	179425815	+	Silent	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179425815A>T	uc010zfg.1	-	275	77564	c.77340T>A	c.(77338-77340)GTT>GTA	p.V25780V	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.V19475V|TTN_uc010zfi.1_Silent_p.V19408V|TTN_uc010zfj.1_Silent_p.V19283V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	26707							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATCATCTTTAACTATAATAG	0.423													39	104	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179437674	179437674	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179437674A>G	uc010zfg.1	-	275	65705	c.65481T>C	c.(65479-65481)TAT>TAC	p.Y21827Y	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.Y15522Y|TTN_uc010zfi.1_Silent_p.Y15455Y|TTN_uc010zfj.1_Silent_p.Y15330Y	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22754							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCGGATCTTATATTCCTGAT	0.493													11	22	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179469036	179469036	+	Intron	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179469036G>T	uc010zfg.1	-						uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCAGATCTAGAAATTAGAAA	0.333													5	29	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179497021	179497021	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179497021G>T	uc010zfg.1	-	185	36120	c.35896C>A	c.(35896-35898)CAG>AAG	p.Q11966K	TTN_uc010zfh.1_Missense_Mutation_p.Q5661K|TTN_uc010zfi.1_Missense_Mutation_p.Q5594K|TTN_uc010zfj.1_Missense_Mutation_p.Q5469K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12893							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTAGGCGCTGGTCATTCTTG	0.438													5	13	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179497022	179497022	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179497022G>T	uc010zfg.1	-	185	36119	c.35895C>A	c.(35893-35895)GAC>GAA	p.D11965E	TTN_uc010zfh.1_Missense_Mutation_p.D5660E|TTN_uc010zfi.1_Missense_Mutation_p.D5593E|TTN_uc010zfj.1_Missense_Mutation_p.D5468E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12892							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTAGGCGCTGGTCATTCTTGA	0.433													5	14	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179556764	179556764	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179556764C>A	uc010zfg.1	-	118	28233	c.28009G>T	c.(28009-28011)GAA>TAA	p.E9337*	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Nonsense_Mutation_p.E5998*|TTN_uc010fre.1_Nonsense_Mutation_p.E448*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	10264							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCAGCAGGTTCCTTCTTAGGC	0.453													15	27	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179588731	179588731	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179588731G>T	uc010zfg.1	-	70	17747	c.17523C>A	c.(17521-17523)GTC>GTA	p.V5841V	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.V2502V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6768							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGCTCCACTGACAATCTTGG	0.433													22	46	---	---	---	---	PASS
MSTN	2660	broad.mit.edu	37	2	190927155	190927155	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190927155A>C	uc002urp.2	-	1	301	c.168T>G	c.(166-168)ATT>ATG	p.I56M		NM_005259	NP_005250	O14793	GDF8_HUMAN	myostatin precursor	56					muscle organ development|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			TTTGTATCTTAATGGCTTCTA	0.388													17	45	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196825422	196825422	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196825422G>A	uc002utj.3	-	18	2554	c.2453C>T	c.(2452-2454)CCA>CTA	p.P818L		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	818	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						CAATGCATATGGAGAATCATG	0.393													25	91	---	---	---	---	PASS
CCDC150	284992	broad.mit.edu	37	2	197521505	197521505	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197521505A>T	uc002utp.1	+	3	460	c.325A>T	c.(325-327)AGC>TGC	p.S109C	CCDC150_uc002uto.1_Missense_Mutation_p.S109C|CCDC150_uc010zgq.1_RNA|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_Intron	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	109	Potential.										0						CCGTCTTGAAAGCCTCATGCA	0.373													23	64	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211541783	211541783	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211541783A>G	uc002vee.3	+	37	4459	c.4327A>G	c.(4327-4329)ACT>GCT	p.T1443A	CPS1_uc010fur.2_Missense_Mutation_p.T1449A|CPS1_uc010fus.2_Missense_Mutation_p.T992A	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	1443					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		CAACAACAACACTAAATTTGT	0.348													22	92	---	---	---	---	PASS
KIF1A	547	broad.mit.edu	37	2	241656788	241656788	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241656788C>T	uc002vzy.2	-	47	5212	c.5066G>A	c.(5065-5067)CGG>CAG	p.R1689Q	KIF1A_uc010fzk.2_Missense_Mutation_p.R1790Q|KIF1A_uc002vzw.2_Missense_Mutation_p.R350Q|KIF1A_uc002vzx.2_Missense_Mutation_p.R416Q	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	1689					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GGTTCAGACCCGCATCTGGGC	0.662													10	17	---	---	---	---	PASS
ITPR1	3708	broad.mit.edu	37	3	4683776	4683776	+	Splice_Site	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4683776G>T	uc003bqa.2	+	7	715	c.367_splice	c.e7-1	p.L123_splice	ITPR1_uc010hbz.2_Splice_Site_p.L123_splice|ITPR1_uc010hca.1_Splice_Site_p.L123_splice|ITPR1_uc011asu.1_Splice_Site_p.L123_splice|ITPR1_uc010hcb.1_Splice_Site_p.L123_splice	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		TGGGTTTTTAGCTCCTGCATT	0.408													25	27	---	---	---	---	PASS
SLC6A6	6533	broad.mit.edu	37	3	14489188	14489188	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14489188A>G	uc010heg.2	+	12	754	c.463A>G	c.(463-465)AAG>GAG	p.K155E	SLC6A6_uc003byp.2_Missense_Mutation_p.K155E|SLC6A6_uc010hef.1_RNA|SLC6A6_uc003byq.2_Missense_Mutation_p.K155E|SLC6A6_uc003byr.2_RNA	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter	155	Extracellular (Potential).				cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1						GTCCTTCCAGAAGGAGCTGCC	0.542													56	141	---	---	---	---	PASS
C3orf19	51244	broad.mit.edu	37	3	14695956	14695956	+	Silent	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14695956C>G	uc003byw.2	+	2	157	c.66C>G	c.(64-66)CTC>CTG	p.L22L	C3orf19_uc010hei.1_Silent_p.L22L	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244	22											0						AGGCTGAACTCTTCCGAAAGC	0.299													4	22	---	---	---	---	PASS
AZI2	64343	broad.mit.edu	37	3	28373873	28373873	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28373873G>C	uc003ceb.2	-	6	1166	c.634C>G	c.(634-636)CTA>GTA	p.L212V	AZI2_uc003cec.2_Missense_Mutation_p.L100V|AZI2_uc003ced.2_Missense_Mutation_p.L212V|AZI2_uc003cee.3_Missense_Mutation_p.L212V|AZI2_uc003ceg.2_Missense_Mutation_p.L212V|AZI2_uc011axd.1_Missense_Mutation_p.L212V|AZI2_uc003cef.2_Missense_Mutation_p.L212V	NM_022461	NP_071906	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2 isoform a	212	Interaction with TBK1.					mitochondrion|plasma membrane				ovary(2)	2						GAAATGCTTAGTTTTTGGAGA	0.313													25	27	---	---	---	---	PASS
TGFBR2	7048	broad.mit.edu	37	3	30713401	30713401	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30713401G>A	uc003ceo.2	+	4	1108	c.726G>A	c.(724-726)CTG>CTA	p.L242L	TGFBR2_uc003cen.2_Silent_p.L267L	NM_003242	NP_003233	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II	242	Cytoplasmic (Potential).				activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis	caveola|external side of plasma membrane	ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding			pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1)	26						CAGAGCTGCTGCCCATTGAGC	0.537													29	19	---	---	---	---	PASS
SUSD5	26032	broad.mit.edu	37	3	33195275	33195275	+	Silent	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33195275T>C	uc003cfo.1	-	5	1267	c.849A>G	c.(847-849)TCA>TCG	p.S283S		NM_015551	NP_056366	O60279	SUSD5_HUMAN	sushi domain containing 5 precursor	283	Extracellular (Potential).				cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2						GTGATCCTGGTGAATCTGCGG	0.537													26	19	---	---	---	---	PASS
ARPP21	10777	broad.mit.edu	37	3	35730842	35730842	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35730842C>A	uc003cgb.2	+	7	714	c.450C>A	c.(448-450)CAC>CAA	p.H150Q	ARPP21_uc003cga.2_Missense_Mutation_p.H150Q|ARPP21_uc011axy.1_Missense_Mutation_p.H150Q|ARPP21_uc003cgf.2_5'Flank	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	150						cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3						TAGACTTACACGAGTTTCTGA	0.353													31	36	---	---	---	---	PASS
ARPP21	10777	broad.mit.edu	37	3	35770811	35770811	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35770811C>T	uc003cgb.2	+	15	1506	c.1242C>T	c.(1240-1242)AGC>AGT	p.S414S	ARPP21_uc003cga.2_Silent_p.S360S|ARPP21_uc011axy.1_Silent_p.S380S|ARPP21_uc003cgf.2_Silent_p.S215S|ARPP21_uc003cgg.2_5'UTR	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	414	Ser-rich.					cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3						AGTCTTCCAGCAGTGCAGGCT	0.527													14	26	---	---	---	---	PASS
LRIG1	26018	broad.mit.edu	37	3	66444471	66444471	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66444471G>T	uc003dmx.2	-	12	1475	c.1461C>A	c.(1459-1461)TTC>TTA	p.F487L	LRIG1_uc011bfu.1_Missense_Mutation_p.F107L|LRIG1_uc003dmw.2_Missense_Mutation_p.F153L|LRIG1_uc010hnz.2_Missense_Mutation_p.F203L|LRIG1_uc010hoa.2_Missense_Mutation_p.F511L	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	487	Extracellular (Potential).|LRRCT.					integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TACCGCACACGAAACTCTCTG	0.493													3	20	---	---	---	---	PASS
PDZRN3	23024	broad.mit.edu	37	3	73433401	73433401	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73433401C>A	uc003dpl.1	-	10	2412	c.2316G>T	c.(2314-2316)GAG>GAT	p.E772D	PDZRN3_uc011bgh.1_Missense_Mutation_p.E429D|PDZRN3_uc010hoe.1_Missense_Mutation_p.E470D|PDZRN3_uc011bgf.1_Missense_Mutation_p.E489D|PDZRN3_uc011bgg.1_Missense_Mutation_p.E492D	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	772							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CGGGGGAGATCTCCAGGGTGA	0.652													4	13	---	---	---	---	PASS
CNTN3	5067	broad.mit.edu	37	3	74413749	74413749	+	Splice_Site	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74413749T>A	uc003dpm.1	-	9	1164	c.1084_splice	c.e9-1	p.E362_splice		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		TGTTCTCTCCTAGATGATAAT	0.328													10	20	---	---	---	---	PASS
DRD3	1814	broad.mit.edu	37	3	113850162	113850162	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113850162T>C	uc003ebd.2	-	7	1232	c.809A>G	c.(808-810)CAA>CGA	p.Q270R	DRD3_uc010hqn.1_Missense_Mutation_p.Q270R|DRD3_uc003ebb.1_Missense_Mutation_p.Q270R|DRD3_uc003ebc.1_Missense_Mutation_p.Q270R	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	270	Cytoplasmic.				activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)	TCCTCTTTCTTGGAAGCCTGG	0.532													22	54	---	---	---	---	PASS
GOLGB1	2804	broad.mit.edu	37	3	121416536	121416536	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121416536C>G	uc003eei.3	-	13	2945	c.2819G>C	c.(2818-2820)AGA>ACA	p.R940T	GOLGB1_uc010hrc.2_Missense_Mutation_p.R945T|GOLGB1_uc003eej.3_Missense_Mutation_p.R906T|GOLGB1_uc011bjm.1_Missense_Mutation_p.R826T|GOLGB1_uc010hrd.1_Missense_Mutation_p.R904T	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	940	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		TTCCTCAGCTCTGGATAATAA	0.358													14	109	---	---	---	---	PASS
CASR	846	broad.mit.edu	37	3	122003472	122003472	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122003472C>G	uc003eev.3	+	7	3043	c.2671C>G	c.(2671-2673)CGC>GGC	p.R891G	CASR_uc003eew.3_Missense_Mutation_p.R901G	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	891	Cytoplasmic (Potential).|Interaction with RNF19A.				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	CACGCTGCGCCGCAGCAACGT	0.627													15	20	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124160916	124160916	+	Intron	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124160916A>G	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GGTCAGTGAGAGACCTGCCCA	0.527													4	20	---	---	---	---	PASS
ALDH1L1	10840	broad.mit.edu	37	3	125831645	125831645	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125831645C>G	uc003eim.1	-	19	2351	c.2161G>C	c.(2161-2163)GAT>CAT	p.D721H	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Missense_Mutation_p.D620H|ALDH1L1_uc003ein.1_Missense_Mutation_p.D256H	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	721	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	ACGAACTCATCATGAATGGAG	0.562													18	106	---	---	---	---	PASS
DBR1	51163	broad.mit.edu	37	3	137881387	137881387	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137881387C>A	uc003erv.2	-	8	1115	c.979G>T	c.(979-981)GTA>TTA	p.V327L	DBR1_uc003eru.2_Missense_Mutation_p.V276L|DBR1_uc003ert.2_Missense_Mutation_p.V95L	NM_016216	NP_057300	Q9UK59	DBR1_HUMAN	debranching enzyme homolog 1	327						nucleus	metal ion binding|RNA lariat debranching enzyme activity				0						TTTTCCAATACTTCTTTCATA	0.333													15	94	---	---	---	---	PASS
PLSCR5	389158	broad.mit.edu	37	3	146309615	146309615	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146309615C>A	uc003ewb.2	-	5	1511	c.507G>T	c.(505-507)TGG>TGT	p.W169C	PLSCR5_uc010hvb.2_Missense_Mutation_p.W157C|PLSCR5_uc010hvc.2_Missense_Mutation_p.W169C	NM_001085420	NP_001078889	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	169											0						GAAAGGGGTCCCACTTCTGCG	0.378													5	44	---	---	---	---	PASS
MED12L	116931	broad.mit.edu	37	3	150874031	150874031	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150874031G>T	uc003eyp.2	+	5	678	c.640G>T	c.(640-642)GAT>TAT	p.D214Y	MED12L_uc011bnz.1_Missense_Mutation_p.D214Y|MED12L_uc003eym.1_Missense_Mutation_p.D214Y|MED12L_uc003eyn.2_Missense_Mutation_p.D214Y|MED12L_uc003eyo.2_Missense_Mutation_p.D214Y	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	214					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAGCACGGGCGATGGCCCTGT	0.473													10	67	---	---	---	---	PASS
SHOX2	6474	broad.mit.edu	37	3	157820671	157820671	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157820671G>A	uc003fbr.2	-	2	490	c.351C>T	c.(349-351)TCC>TCT	p.S117S	SHOX2_uc003fbs.2_Silent_p.S141S|SHOX2_uc010hvw.2_Silent_p.S117S	NM_006884	NP_006875	O60902	SHOX2_HUMAN	short stature homeobox 2 isoform a	117					nervous system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TCAGCTCCGGGGACACTGGAG	0.483													13	82	---	---	---	---	PASS
YEATS2	55689	broad.mit.edu	37	3	183454574	183454574	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183454574A>T	uc003fly.2	+	8	1076	c.881A>T	c.(880-882)AAG>ATG	p.K294M		NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	294	YEATS.				histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GTTCATTTTAAGGACAGCCAG	0.403													22	152	---	---	---	---	PASS
TPRG1	285386	broad.mit.edu	37	3	188956624	188956624	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188956624G>T	uc003frv.1	+	9	1632	c.405G>T	c.(403-405)CTG>CTT	p.L135L	TPRG1_uc003frw.1_Silent_p.L135L	NM_198485	NP_940887	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	135											0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		GTGTGCAGCTGCAGCGGATTC	0.473													34	105	---	---	---	---	PASS
CLDN16	10686	broad.mit.edu	37	3	190126254	190126254	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190126254G>C	uc003fsi.2	+	4	812	c.744G>C	c.(742-744)TTG>TTC	p.L248F	CLDN16_uc010hze.2_Intron	NM_006580	NP_006571	Q9Y5I7	CLD16_HUMAN	claudin 16	248	Helical; (Potential).				calcium-independent cell-cell adhesion|cellular metal ion homeostasis|excretion	integral to membrane|tight junction	identical protein binding|magnesium ion transmembrane transporter activity|structural molecule activity			ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		GTTGCTTTTTGGCTGGAGCTG	0.388													13	92	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193130151	193130151	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193130151T>A	uc003ftd.2	-	27	3132	c.3024A>T	c.(3022-3024)ACA>ACT	p.T1008T	ATP13A4_uc010hzi.2_RNA	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1008	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CATTTTGTACTGTGCAGGCAC	0.393													59	179	---	---	---	---	PASS
CPN2	1370	broad.mit.edu	37	3	194062580	194062580	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194062580G>A	uc003fts.2	-	2	942	c.852C>T	c.(850-852)CTC>CTT	p.L284L		NM_001080513	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	284	LRR 8.				protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		TGTGGGCAAAGAGGCCGGCAG	0.612													8	62	---	---	---	---	PASS
IQCG	84223	broad.mit.edu	37	3	197670685	197670685	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197670685C>A	uc003fyo.2	-	3	392	c.246G>T	c.(244-246)ATG>ATT	p.M82I	IQCG_uc003fyp.2_Missense_Mutation_p.M82I|IQCG_uc003fyq.3_Missense_Mutation_p.M82I	NM_001134435	NP_001127907	Q9H095	IQCG_HUMAN	IQ motif containing G	82											0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		ACTGAACGGGCATGATGTAGT	0.468													22	151	---	---	---	---	PASS
ZNF595	152687	broad.mit.edu	37	4	86295	86295	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86295G>C	uc003fzv.1	+	6	1057	c.901G>C	c.(901-903)GAA>CAA	p.E301Q	ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc011bus.1_Missense_Mutation_p.E69Q|ZNF595_uc011but.1_Missense_Mutation_p.E69Q	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595	301					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		AAGCCTGAATGAACATAAGAA	0.378													16	39	---	---	---	---	PASS
CTBP1	1487	broad.mit.edu	37	4	1206732	1206732	+	Missense_Mutation	SNP	C	A	A	rs7687296	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1206732C>A	uc003gcv.1	-	8	1273	c.1108G>T	c.(1108-1110)GTG>TTG	p.V370L	uc003gcs.1_Intron|CTBP1_uc003gct.1_Missense_Mutation_p.V351L|CTBP1_uc003gcu.1_Missense_Mutation_p.V359L|CTBP1_uc003gcw.2_Missense_Mutation_p.V44L	NM_001328	NP_001319	Q13363	CTBP1_HUMAN	C-terminal binding protein 1 isoform 1	370					interspecies interaction between organisms|negative regulation of cell proliferation|negative regulation of histone H4 acetylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|protein phosphorylation|regulation of cell cycle|regulation of transcription by chromatin organization|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|viral genome replication|white fat cell differentiation	cytoplasm|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein C-terminus binding|protein domain specific binding|transcription factor binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		TCAGGGTGCACGACGGCGGGG	0.657													4	17	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20618590	20618590	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20618590C>A	uc003gpr.1	+	35	4109	c.3905C>A	c.(3904-3906)ACC>AAC	p.T1302N	SLIT2_uc003gps.1_Missense_Mutation_p.T1294N	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	1302	Laminin G-like.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						CAGAACGGAACCAGCTTCCAC	0.587													11	48	---	---	---	---	PASS
N4BP2	55728	broad.mit.edu	37	4	40123482	40123482	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40123482C>T	uc003guy.3	+	9	4089	c.3751C>T	c.(3751-3753)CCA>TCA	p.P1251S	N4BP2_uc010ifq.2_Missense_Mutation_p.P1171S|N4BP2_uc010ifr.2_Missense_Mutation_p.P1171S	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2	1251						cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						GCAGTCCTTTCCAGGTATTCT	0.373													25	96	---	---	---	---	PASS
ATP10D	57205	broad.mit.edu	37	4	47514816	47514816	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47514816G>C	uc003gxk.1	+	2	423	c.259G>C	c.(259-261)GTG>CTG	p.V87L	ATP10D_uc003gxj.3_Missense_Mutation_p.V87L	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	87	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3						TCTGAATTTTGTGCCAAGAAA	0.333													11	37	---	---	---	---	PASS
CORIN	10699	broad.mit.edu	37	4	47682236	47682236	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47682236C>G	uc003gxm.2	-	8	1147	c.1054G>C	c.(1054-1056)GAC>CAC	p.D352H	CORIN_uc011bzf.1_Missense_Mutation_p.D213H|CORIN_uc011bzg.1_Missense_Mutation_p.D285H|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron|CORIN_uc003gxn.3_3'UTR	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	352	Extracellular (Potential).|LDL-receptor class A 3.				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2						CAGCGCCCGTCCCCGCAGCGA	0.542													10	30	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66231739	66231739	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66231739T>C	uc003hcy.2	-	11	2154	c.1961A>G	c.(1960-1962)CAT>CGT	p.H654R	EPHA5_uc003hcx.2_Missense_Mutation_p.H586R|EPHA5_uc003hcz.2_Missense_Mutation_p.H632R|EPHA5_uc011cah.1_Missense_Mutation_p.H655R|EPHA5_uc011cai.1_Missense_Mutation_p.H633R|EPHA5_uc003hda.2_Missense_Mutation_p.H655R	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	654	Cytoplasmic (Potential).				cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						CTCATAGGTATGTGGATCAAT	0.373										TSP Lung(17;0.13)			25	34	---	---	---	---	PASS
UGT2A3	79799	broad.mit.edu	37	4	69816854	69816854	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69816854C>G	uc003hef.2	-	1	656	c.625G>C	c.(625-627)GTA>CTA	p.V209L	UGT2A3_uc010ihp.1_RNA	NM_024743	NP_079019	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family,	209	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(1)|skin(1)	2						GAATTTTTTACTCTTTCCAGA	0.403													13	30	---	---	---	---	PASS
ENAM	10117	broad.mit.edu	37	4	71497560	71497560	+	Intron	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71497560T>A	uc011caw.1	+							NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor						bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)			ATTCTCTTACTTCCAGATGCA	0.403													31	83	---	---	---	---	PASS
ENAM	10117	broad.mit.edu	37	4	71509397	71509397	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71509397G>A	uc011caw.1	+	9	2535	c.2254G>A	c.(2254-2256)GCT>ACT	p.A752T		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	752					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)			TAATAATGCCGCTGGACCAGA	0.453													21	51	---	---	---	---	PASS
RRH	10692	broad.mit.edu	37	4	110765235	110765235	+	Intron	SNP	G	T	T	rs140795458	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110765235G>T	uc003hzv.2	+							NM_006583	NP_006574	O14718	OPSX_HUMAN	peropsin						phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		TTTTTTTATCGTAGGTTTCGG	0.383													18	73	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113462282	113462282	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113462282G>A	uc003iau.2	-	25	5952	c.5741C>T	c.(5740-5742)ACC>ATC	p.T1914I	C4orf21_uc003iav.2_RNA|C4orf21_uc003iat.2_Missense_Mutation_p.T372I	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	736						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		AAAACACAGGGTTGGTAGCCA	0.378													5	11	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114195750	114195750	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114195750T>C	uc003ibe.3	+	15	1728	c.1628T>C	c.(1627-1629)GTG>GCG	p.V543A	ANK2_uc003ibd.3_Missense_Mutation_p.V522A|ANK2_uc003ibf.3_Missense_Mutation_p.V543A|ANK2_uc003ibc.2_Missense_Mutation_p.V519A|ANK2_uc011cgb.1_Missense_Mutation_p.V558A	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	543	ANK 16.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GAGGGCCAGGTGGATGTGGCA	0.512													14	43	---	---	---	---	PASS
IL21	59067	broad.mit.edu	37	4	123542049	123542049	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123542049G>T	uc003ies.2	-	1	163	c.118C>A	c.(118-120)CGT>AGT	p.R40S	uc003iet.2_RNA|IL21_uc010int.2_Missense_Mutation_p.R33S	NM_021803	NP_068575	Q9HBE4	IL21_HUMAN	interleukin 21	33					cell maturation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-17 production|positive regulation of T cell proliferation|signal transduction	extracellular space	cytokine activity|interleukin-2 receptor binding				0						ATAAGTTGACGCATTCTAATC	0.368													11	54	---	---	---	---	PASS
NPY2R	4887	broad.mit.edu	37	4	156135368	156135368	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156135368G>T	uc003ioq.2	+	2	772	c.277G>T	c.(277-279)GCT>TCT	p.A93S	NPY2R_uc003ior.2_Missense_Mutation_p.A93S	NM_000910	NP_000901	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	93	Helical; Name=2; (Potential).				cardiac left ventricle morphogenesis|inhibition of adenylate cyclase activity by G-protein signaling pathway|locomotory behavior|outflow tract morphogenesis	integral to plasma membrane	calcium channel regulator activity			lung(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0854)				TGCCAATCTGGCTGTGGCAGA	0.473													4	24	---	---	---	---	PASS
GRIA2	2891	broad.mit.edu	37	4	158224786	158224786	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158224786C>T	uc003ipm.3	+	3	771	c.312C>T	c.(310-312)TGC>TGT	p.C104C	GRIA2_uc011cit.1_Silent_p.C57C|GRIA2_uc003ipl.3_Silent_p.C104C|GRIA2_uc003ipk.3_Silent_p.C57C|GRIA2_uc010iqh.1_RNA	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2	104	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)	CATCATTTTGCGGAACACTCC	0.433													25	95	---	---	---	---	PASS
C4orf46	201725	broad.mit.edu	37	4	159590809	159590809	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159590809C>G	uc003iqa.2	-	2	547	c.298G>C	c.(298-300)GAC>CAC	p.D100H	C4orf46_uc010iqp.1_RNA|ETFDH_uc010iqq.2_5'Flank|ETFDH_uc003iqb.2_5'Flank|ETFDH_uc011cjg.1_5'Flank|ETFDH_uc010iqr.2_5'Flank	NM_001008393	NP_001008394	Q504U0	CD046_HUMAN	hypothetical protein LOC201725	100										skin(1)	1						TTCAAGAGGTCCCGCCACGTT	0.378													13	38	---	---	---	---	PASS
RAPGEF2	9693	broad.mit.edu	37	4	160251607	160251607	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160251607A>G	uc003iqg.3	+	7	1251	c.941A>G	c.(940-942)AAA>AGA	p.K314R		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	314	N-terminal Ras-GEF.				cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GAAGTGGGCAAAAAGTTATTG	0.363													14	59	---	---	---	---	PASS
FSTL5	56884	broad.mit.edu	37	4	162697178	162697178	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162697178A>G	uc003iqh.2	-	5	894	c.458T>C	c.(457-459)TTA>TCA	p.L153S	FSTL5_uc003iqi.2_Missense_Mutation_p.L152S|FSTL5_uc010iqv.2_Missense_Mutation_p.L152S	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	153						extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TTGTAAATCTAATAGCATATT	0.284													9	21	---	---	---	---	PASS
FSTL5	56884	broad.mit.edu	37	4	162697198	162697198	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162697198G>T	uc003iqh.2	-	5	874	c.438C>A	c.(436-438)AGC>AGA	p.S146R	FSTL5_uc003iqi.2_Missense_Mutation_p.S145R|FSTL5_uc010iqv.2_Missense_Mutation_p.S145R	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	146						extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TTTTCATCTTGCTGTATTCAG	0.279													6	19	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175897228	175897228	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175897228T>A	uc003iuc.2	+	5	1222	c.552T>A	c.(550-552)ACT>ACA	p.T184T	ADAM29_uc003iud.2_Silent_p.T184T|ADAM29_uc010irr.2_Silent_p.T184T|ADAM29_uc011cki.1_Silent_p.T184T	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	184					proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		ATAATTCCACTCAGAAGCAAA	0.358													14	28	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	225549	225549	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:225549G>T	uc003jao.3	+	4	443	c.328G>T	c.(328-330)GCT>TCT	p.A110S	SDHA_uc003jan.2_Missense_Mutation_p.A110S|SDHA_uc011clv.1_Missense_Mutation_p.A110S|SDHA_uc011clw.1_Intron|SDHA_uc003jap.3_Missense_Mutation_p.A110S|SDHA_uc003jaq.3_5'Flank	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,	110					nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	AATCAATGCTGCTCTGGGGAA	0.567									Familial_Paragangliomas				21	77	---	---	---	---	PASS
NSUN2	54888	broad.mit.edu	37	5	6620312	6620312	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6620312T>C	uc003jdu.2	-	7	787	c.722A>G	c.(721-723)CAT>CGT	p.H241R	NSUN2_uc003jdt.2_Missense_Mutation_p.H5R|NSUN2_uc011cmk.1_Missense_Mutation_p.H206R|NSUN2_uc003jdv.2_Missense_Mutation_p.H5R	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2	241						cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						GGAGGCATCATGGTTGACCAC	0.498													12	79	---	---	---	---	PASS
PAPD7	11044	broad.mit.edu	37	5	6755026	6755026	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6755026C>G	uc003jdx.1	+	13	1726	c.1597C>G	c.(1597-1599)CGG>GGG	p.R533G	PAPD7_uc011cmn.1_Missense_Mutation_p.R523G|PAPD7_uc010itl.1_Missense_Mutation_p.R353G	NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma	533					cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1						CACACACACACGGGACAGTCT	0.662													10	19	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21760770	21760770	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21760770G>T	uc010iuc.2	-	10	1988	c.1530C>A	c.(1528-1530)GTC>GTA	p.V510V	CDH12_uc011cno.1_Silent_p.V470V|CDH12_uc003jgk.2_Silent_p.V510V|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	510	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						CTGCAGCACTGACTATCTGAA	0.403										HNSCC(59;0.17)			28	111	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21975451	21975451	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21975451G>T	uc010iuc.2	-	3	733	c.275C>A	c.(274-276)ACC>AAC	p.T92N	CDH12_uc011cno.1_Missense_Mutation_p.T92N|CDH12_uc003jgk.2_Missense_Mutation_p.T92N	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	92	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						TCCTGAGAGGGTGTATTTCAC	0.368										HNSCC(59;0.17)			19	80	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	22078648	22078648	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22078648C>A	uc010iuc.2	-	2	596	c.138G>T	c.(136-138)CGG>CGT	p.R46R	CDH12_uc011cno.1_Silent_p.R46R|CDH12_uc003jgk.2_Silent_p.R46R	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	46					adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						GGAAATGTGACCGTTGTCCTG	0.473										HNSCC(59;0.17)			38	154	---	---	---	---	PASS
RXFP3	51289	broad.mit.edu	37	5	33936910	33936910	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33936910C>G	uc003jic.1	+	1	422	c.65C>G	c.(64-66)GCA>GGA	p.A22G		NM_016568	NP_057652	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	22	Extracellular (Potential).					integral to plasma membrane	N-formyl peptide receptor activity			upper_aerodigestive_tract(1)	1						GACAAGCTAGCAGAACTCTTC	0.607													11	56	---	---	---	---	PASS
UGT3A1	133688	broad.mit.edu	37	5	35965865	35965865	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35965865C>T	uc003jjv.1	-	4	623	c.466G>A	c.(466-468)GAG>AAG	p.E156K	UGT3A1_uc003jjw.1_RNA|UGT3A1_uc011coq.1_Missense_Mutation_p.E156K|UGT3A1_uc011cor.1_Missense_Mutation_p.E122K|UGT3A1_uc003jjy.1_Missense_Mutation_p.E102K	NM_152404	NP_689617	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	156	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|central_nervous_system(1)	3	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACAAGCTTCTCAGCAATCAGG	0.398													20	62	---	---	---	---	PASS
UGT3A2	167127	broad.mit.edu	37	5	36035849	36035849	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36035849C>T	uc003jjz.1	-	7	1616	c.1523G>A	c.(1522-1524)GGC>GAC	p.G508D	UGT3A2_uc011cos.1_Missense_Mutation_p.G474D|UGT3A2_uc011cot.1_Missense_Mutation_p.G206D	NM_174914	NP_777574	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	508	Cytoplasmic (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GACAGCCATGCCCAGCAGCTT	0.582													5	34	---	---	---	---	PASS
CARD6	84674	broad.mit.edu	37	5	40852718	40852718	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40852718G>T	uc003jmg.2	+	3	1359	c.1284G>T	c.(1282-1284)GTG>GTT	p.V428V		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	428					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5						AAGACATTGTGAAGAAGCAGT	0.453													19	66	---	---	---	---	PASS
C7	730	broad.mit.edu	37	5	40972654	40972654	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40972654A>G	uc003jmh.2	+	15	2146	c.2032A>G	c.(2032-2034)AAG>GAG	p.K678E	C7_uc011cpn.1_RNA	NM_000587	NP_000578	P10643	CO7_HUMAN	complement component 7 precursor	678	Sushi 2.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)				CTCCAGCCTTAAGTGGAGTCC	0.488													25	174	---	---	---	---	PASS
TAF9	6880	broad.mit.edu	37	5	68661332	68661332	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68661332C>A	uc003jwc.1	-	2	565	c.233G>T	c.(232-234)CGC>CTC	p.R78L	TAF9_uc003jwa.2_Intron|TAF9_uc003jwb.2_Intron|TAF9_uc003jwd.1_Missense_Mutation_p.R78L|TAF9_uc003jwe.1_Missense_Mutation_p.R78L|TAF9_uc003jwf.1_Missense_Mutation_p.R78L	NM_003187	NP_003178	Q16594	TAF9_HUMAN	TAF9 RNA polymerase II, TATA box binding	78					histone H3 acetylation|negative regulation of apoptosis|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of cell growth|positive regulation of response to cytokine stimulus|positive regulation of transcription from RNA polymerase II promoter|response to interleukin-1|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	MLL1 complex|PCAF complex|pre-snoRNP complex|STAGA complex|transcription factor TFIID complex|transcription factor TFTC complex	activating transcription factor binding|C2H2 zinc finger domain binding|p53 binding|transcription coactivator activity|transcription regulatory region DNA binding				0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.1e-56)|Epithelial(20;9.54e-53)|all cancers(19;2.2e-48)|Lung(70;0.0176)		CTGATCAGCGCGGCACTGGAT	0.408													20	51	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70806636	70806636	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70806636G>T	uc003kbp.1	+	17	3980	c.3717G>T	c.(3715-3717)AAG>AAT	p.K1239N	BDP1_uc003kbn.1_Missense_Mutation_p.K1239N|BDP1_uc003kbo.2_Missense_Mutation_p.K1239N	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	1239	Potential.|9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.|8; approximate.				regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AAAGGGAAAAGGTGCTAGCAG	0.403													7	137	---	---	---	---	PASS
AQPEP	206338	broad.mit.edu	37	5	115336143	115336143	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115336143C>A	uc003kro.2	+	8	1693	c.1529C>A	c.(1528-1530)GCC>GAC	p.A510D	AQPEP_uc003krp.2_RNA|AQPEP_uc003krq.2_RNA|AQPEP_uc003krr.2_RNA|AQPEP_uc003krs.2_RNA	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	510	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						GCGTCTATGGCCCGGATGCTT	0.378													18	43	---	---	---	---	PASS
AQPEP	206338	broad.mit.edu	37	5	115336144	115336144	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115336144C>A	uc003kro.2	+	8	1694	c.1530C>A	c.(1528-1530)GCC>GCA	p.A510A	AQPEP_uc003krp.2_RNA|AQPEP_uc003krq.2_RNA|AQPEP_uc003krr.2_RNA|AQPEP_uc003krs.2_RNA	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	510	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						CGTCTATGGCCCGGATGCTTT	0.378													18	42	---	---	---	---	PASS
CDKL3	51265	broad.mit.edu	37	5	133638306	133638306	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133638306A>G	uc003kzf.3	-	12	1813	c.1694T>C	c.(1693-1695)GTG>GCG	p.V565A	CDKL3_uc011cxm.1_Missense_Mutation_p.V372A|CDKL3_uc011cxn.1_RNA|CDKL3_uc010jdw.2_Missense_Mutation_p.V172A|CDKL3_uc011cxo.1_Missense_Mutation_p.V270A|CDKL3_uc011cxp.1_Missense_Mutation_p.V270A|CDKL3_uc011cxq.1_Missense_Mutation_p.V372A	NM_001113575	NP_001107047	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3 isoform 1	565						cytoplasm	ATP binding|cyclin-dependent protein kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATTTTGATCCACGTTAAGTAA	0.299													3	4	---	---	---	---	PASS
CDC25C	995	broad.mit.edu	37	5	137621721	137621721	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137621721G>A	uc003lcp.1	-	13	1533	c.1262C>T	c.(1261-1263)CCA>CTA	p.P421L	CDC25C_uc003lcq.1_Missense_Mutation_p.P348L|CDC25C_uc003lcr.1_Missense_Mutation_p.P421L|CDC25C_uc011cyp.1_Missense_Mutation_p.P438L|CDC25C_uc003lcs.1_Missense_Mutation_p.P499L	NM_001790	NP_001781	P30307	MPIP3_HUMAN	cell division cycle 25C isoform a	421	Rhodanese.				cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm	protein tyrosine phosphatase activity|WW domain binding			lung(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CATATATTCTGGAAAGAAGTC	0.502													18	41	---	---	---	---	PASS
ETF1	2107	broad.mit.edu	37	5	137878583	137878583	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137878583C>T	uc003ldc.3	-	2	190	c.25G>A	c.(25-27)GAC>AAC	p.D9N	ETF1_uc011cyv.1_5'Flank|ETF1_uc010jex.2_RNA|ETF1_uc003ldd.3_5'UTR	NM_004730	NP_004721	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	9					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation|regulation of translational termination	cytoplasm	protein binding|ribosome binding|translation release factor activity, codon specific			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACGTTCCTGTCGGCAGCACTG	0.667													11	10	---	---	---	---	PASS
HARS2	23438	broad.mit.edu	37	5	140075439	140075439	+	Intron	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140075439A>G	uc003lgx.2	+						HARS2_uc010jfv.1_Silent_p.P144P|HARS2_uc011czr.1_Intron|HARS2_uc011czs.1_Intron|HARS2_uc011czt.1_Intron|HARS2_uc011czu.1_Intron	NM_012208	NP_036340	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2 precursor						histidyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|histidine-tRNA ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTGAGGCCAGGGCTGAGAA	0.473													12	22	---	---	---	---	PASS
PCDHA2	56146	broad.mit.edu	37	5	140176677	140176677	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140176677C>T	uc003lhd.2	+	1	2234	c.2128C>T	c.(2128-2130)CTG>TTG	p.L710L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.L710L|PCDHA2_uc011czy.1_Silent_p.L710L	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	710	Helical; (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTATCCAGCCTGTTGGTGCT	0.682													23	48	---	---	---	---	PASS
PCDHA3	56145	broad.mit.edu	37	5	140182453	140182453	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182453C>T	uc003lhf.2	+	1	1671	c.1671C>T	c.(1669-1671)GAC>GAT	p.D557D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.D557D	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	557	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCGTGCTGGACGAGAACGACA	0.687													18	41	---	---	---	---	PASS
DIAPH1	1729	broad.mit.edu	37	5	140966626	140966626	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140966626G>C	uc003llb.3	-	3	424	c.283C>G	c.(283-285)CTC>GTC	p.L95V	DIAPH1_uc003llc.3_Missense_Mutation_p.L86V	NM_005219	NP_005210	O60610	DIAP1_HUMAN	diaphanous 1 isoform 1	95	GBD/FH3.				regulation of microtubule-based process|sensory perception of sound	cytoplasm|cytoskeleton|ruffle membrane	actin binding|receptor binding|Rho GTPase binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTCAAAGAGAACCAGCACT	0.428													25	45	---	---	---	---	PASS
ABLIM3	22885	broad.mit.edu	37	5	148577924	148577924	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148577924C>A	uc003lpy.2	+	4	545	c.294C>A	c.(292-294)GGC>GGA	p.G98G	ABLIM3_uc003lpz.1_Silent_p.G98G|ABLIM3_uc003lqa.1_Missense_Mutation_p.A80D|ABLIM3_uc003lqb.2_Silent_p.G98G|ABLIM3_uc003lqc.1_Silent_p.G98G|ABLIM3_uc003lqd.1_Silent_p.G98G|ABLIM3_uc003lqf.2_Silent_p.G98G|ABLIM3_uc003lqe.1_Silent_p.G98G	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	98	LIM zinc-binding 2.				axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCCCTGGGCCGCACTTACC	0.632													9	14	---	---	---	---	PASS
GABRA6	2559	broad.mit.edu	37	5	161128573	161128573	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161128573G>T	uc003lyu.2	+	9	1494	c.1156G>T	c.(1156-1158)GAG>TAG	p.E386*	GABRA6_uc003lyv.2_Nonsense_Mutation_p.E157*	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	386	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	TTCATCTTCCGAGGCCAATAA	0.453										TCGA Ovarian(5;0.080)			27	30	---	---	---	---	PASS
ATP6V0E1	8992	broad.mit.edu	37	5	172421775	172421775	+	Intron	SNP	T	C	C	rs55955908		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172421775T>C	uc003mcd.1	+							NM_003945	NP_003936	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0						ATP hydrolysis coupled proton transport|cell growth|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport|vacuolar acidification	endosome membrane|integral to membrane|membrane fraction|proton-transporting V-type ATPase, V0 domain|vacuole	proton-transporting ATPase activity, rotational mechanism				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTTTTTTTTTTAGAGTTATCA	0.323													4	4	---	---	---	---	PASS
BMP5	653	broad.mit.edu	37	6	55620414	55620414	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55620414A>G	uc003pcq.2	-	7	1994	c.1282T>C	c.(1282-1284)TCT>CCT	p.S428P	BMP5_uc011dxf.1_Missense_Mutation_p.S391P	NM_021073	NP_066551	P22003	BMP5_HUMAN	bone morphogenetic protein 5 preproprotein	428					cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TACAGAACAGAGATGGCATTT	0.348													27	30	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56335002	56335002	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56335002T>A	uc003pdf.2	-	90	16071	c.16043A>T	c.(16042-16044)TAT>TTT	p.Y5348F	DST_uc003pcz.3_Missense_Mutation_p.Y5170F|DST_uc011dxj.1_Missense_Mutation_p.Y5199F|DST_uc011dxk.1_Missense_Mutation_p.Y5210F|DST_uc003pcy.3_Missense_Mutation_p.Y4844F|DST_uc003pcw.3_5'Flank|DST_uc003pcx.3_5'Flank	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	7256	EF-hand 2.|2 (Potential).				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TACAAATTCATAGTAGTCAAT	0.403													17	14	---	---	---	---	PASS
RWDD2A	112611	broad.mit.edu	37	6	83905545	83905545	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83905545T>C	uc003pjx.3	+	3	704	c.433T>C	c.(433-435)TCT>CCT	p.S145P	PGM3_uc003pjv.2_5'Flank|PGM3_uc003pjw.2_5'Flank|PGM3_uc011dyz.1_5'Flank|RWDD2A_uc011dza.1_Missense_Mutation_p.S70P	NM_033411	NP_219479	Q9UIY3	RWD2A_HUMAN	RWD domain containing 2A	145											0		all_cancers(76;2.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00217)		BRCA - Breast invasive adenocarcinoma(397;0.045)		ATATGAACCATCTACACAAGC	0.428													41	66	---	---	---	---	PASS
C6orf165	154313	broad.mit.edu	37	6	88173891	88173891	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88173891G>T	uc003plv.2	+	13	1884	c.1792G>T	c.(1792-1794)GCT>TCT	p.A598S	SLC35A1_uc003plx.2_RNA|C6orf165_uc003plw.2_Missense_Mutation_p.A410S|C6orf165_uc010kbv.1_RNA	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1	598										central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GATTTACTTGGCTGGTCTTCG	0.468													16	40	---	---	---	---	PASS
FUT9	10690	broad.mit.edu	37	6	96651800	96651800	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96651800C>T	uc003pop.3	+	3	1110	c.769C>T	c.(769-771)CTA>TTA	p.L257L		NM_006581	NP_006572	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3)	257	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		CACGGAAAAGCTATACAATGC	0.343													8	26	---	---	---	---	PASS
ASCC3	10973	broad.mit.edu	37	6	101307057	101307057	+	Intron	SNP	T	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101307057T>G	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron|ASCC3_uc010kcv.2_Intron|ASCC3_uc003pqm.2_Missense_Mutation_p.K88T	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		cagcctcctcttctggaatgg	0.005													15	43	---	---	---	---	PASS
PREP	5550	broad.mit.edu	37	6	105825364	105825364	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105825364C>G	uc003prc.2	-	3	354	c.151G>C	c.(151-153)GTG>CTG	p.V51L		NM_002726	NP_002717	P48147	PPCE_HUMAN	prolyl endopeptidase	51					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AGAAATGGCACAGTAATCTTA	0.353													17	38	---	---	---	---	PASS
AIM1	202	broad.mit.edu	37	6	106973217	106973217	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106973217T>A	uc003prh.2	+	4	3631	c.3144T>A	c.(3142-3144)TCT>TCA	p.S1048S		NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	1048	Beta/gamma crystallin 'Greek key' 1.						sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		ATTGCAGTTCTTGGAGCCTCT	0.398													34	67	---	---	---	---	PASS
TAAR6	319100	broad.mit.edu	37	6	132891957	132891957	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132891957C>A	uc011eck.1	+	1	497	c.497C>A	c.(496-498)GCT>GAT	p.A166D		NM_175067	NP_778237	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	166	Helical; Name=4; (Potential).					plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(1)	3	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		TACAGCGGTGCTGTGTTCTAC	0.502													67	117	---	---	---	---	PASS
HBS1L	10767	broad.mit.edu	37	6	135300358	135300358	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135300358T>C	uc003qez.2	-	14	1853	c.1646A>G	c.(1645-1647)CAT>CGT	p.H549R	HBS1L_uc003qey.2_Missense_Mutation_p.H385R|HBS1L_uc011ecy.1_Missense_Mutation_p.H273R|HBS1L_uc011ecz.1_Missense_Mutation_p.H385R|HBS1L_uc011eda.1_Missense_Mutation_p.H507R	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein	549					signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AAGACTAACATGATCGCCTGC	0.428													7	37	---	---	---	---	PASS
SASH1	23328	broad.mit.edu	37	6	148865626	148865626	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148865626C>T	uc003qme.1	+	18	3495	c.3020C>T	c.(3019-3021)CCC>CTC	p.P1007L	SASH1_uc011eeb.1_Missense_Mutation_p.P768L|SASH1_uc003qmf.1_Missense_Mutation_p.P417L	NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	1007	Pro-rich.						protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		CCCATGGGCCCCAGTGGGGCC	0.632													16	20	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152527420	152527420	+	Silent	SNP	C	T	T	rs140577642		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152527420C>T	uc010kiw.2	-	126	23504	c.22902G>A	c.(22900-22902)TCG>TCA	p.S7634S	SYNE1_uc010kiv.2_Silent_p.S2158S|SYNE1_uc003qos.3_Silent_p.S2158S|SYNE1_uc003qot.3_Silent_p.S7563S|SYNE1_uc003qou.3_Silent_p.S7634S|SYNE1_uc003qor.3_Silent_p.S534S	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7634	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CACTGTCCGCCGAGAGAAGGA	0.507										HNSCC(10;0.0054)			10	25	---	---	---	---	PASS
IPCEF1	26034	broad.mit.edu	37	6	154533895	154533895	+	Intron	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154533895G>T	uc003qpx.2	-						OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpv.2_Intron|IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0						TACTTATGTCGGTACATACCA	0.418													3	16	---	---	---	---	PASS
LPAL2	80350	broad.mit.edu	37	6	160913805	160913805	+	Intron	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160913805C>A	uc003qtj.2	-						LPAL2_uc011efy.1_Intron	NR_028093				Homo sapiens cDNA FLJ43922 fis, clone TESTI4012406.												0		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)		TGGCCACAGACTTCTTACCTT	0.488													27	95	---	---	---	---	PASS
GLCCI1	113263	broad.mit.edu	37	7	8124623	8124623	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8124623G>C	uc003srk.2	+	7	1833	c.1274G>C	c.(1273-1275)CGA>CCA	p.R425P		NM_138426	NP_612435	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	425											0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		GGATGTGAGCGAGTGAAGGTC	0.458													8	29	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21757518	21757518	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21757518C>G	uc003svc.2	+	44	7161	c.7130C>G	c.(7129-7131)TCA>TGA	p.S2377*		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2377					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						ACCATCACTTCAATTCCTGAG	0.408									Kartagener_syndrome				29	63	---	---	---	---	PASS
STK31	56164	broad.mit.edu	37	7	23775399	23775399	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23775399G>T	uc003sws.3	+	7	793	c.726G>T	c.(724-726)TTG>TTT	p.L242F	STK31_uc003swt.3_Missense_Mutation_p.L219F|STK31_uc011jze.1_Missense_Mutation_p.L242F|STK31_uc010kuq.2_Missense_Mutation_p.L219F	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	242							ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						CCATTCCTTTGTGGGGGCATA	0.453													12	41	---	---	---	---	PASS
AQP1	358	broad.mit.edu	37	7	30951557	30951557	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30951557G>T	uc003tbv.1	+	1	90	c.33G>T	c.(31-33)TGG>TGT	p.W11C	AQP1_uc011kac.1_Intron	NM_198098	NP_932766	P29972	AQP1_HUMAN	aquaporin 1	11	Helical; Name=Helix 1.				ammonium transport|cell volume homeostasis|cellular hyperosmotic response|cellular response to cAMP|cellular response to copper ion|cellular response to dexamethasone stimulus|cellular response to hydrogen peroxide|cellular response to hypoxia|cellular response to mechanical stimulus|cellular response to mercury ion|cellular response to nitric oxide|cellular response to retinoic acid|cellular response to salt stress|cellular response to UV|cerebrospinal fluid secretion|cGMP biosynthetic process|establishment or maintenance of actin cytoskeleton polarity|lateral ventricle development|maintenance of symbiont-containing vacuole via substance secreted by host|negative regulation of apoptosis|odontogenesis|pancreatic juice secretion|positive regulation of angiogenesis|positive regulation of fibroblast proliferation|positive regulation of saliva secretion|renal water transport|response to drug|transepithelial water transport	apical plasma membrane|basal plasma membrane|brush border membrane|cytoplasm|integral to plasma membrane|nuclear membrane|sarcolemma|symbiont-containing vacuole	ammonia transmembrane transporter activity|carbon dioxide transmembrane transporter activity|glycerol transmembrane transporter activity|intracellular cGMP activated cation channel activity|nitric oxide transmembrane transporter activity|potassium channel activity|potassium ion transmembrane transporter activity|protein binding|water channel activity				0		Melanoma(862;0.16)			Acetazolamide(DB00819)	AGCTCTTCTGGAGGGCAGTGG	0.612													4	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	38402737	38402737	+	Intron	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38402737A>T	uc003tgp.1	+						uc003tgs.1_Missense_Mutation_p.S28T					Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																		CTGATGACTGACTTCGTTCTC	0.463													21	58	---	---	---	---	PASS
MRPS24	64951	broad.mit.edu	37	7	43906368	43906368	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43906368T>C	uc003tit.1	-	4	485	c.434A>G	c.(433-435)TAC>TGC	p.Y145C		NM_032014	NP_114403	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24 precursor	145					translation	mitochondrial large ribosomal subunit|mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0						TTTGTAAAAGTAGGACAGCAA	0.493													15	41	---	---	---	---	PASS
DBNL	28988	broad.mit.edu	37	7	44099661	44099661	+	Silent	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44099661T>C	uc003tjp.3	+	12	1160	c.1062T>C	c.(1060-1062)GGT>GGC	p.G354G	DBNL_uc003tjo.3_Silent_p.G355G|DBNL_uc003tjr.3_Silent_p.G227G|DBNL_uc003tjq.3_Silent_p.G363G|DBNL_uc011kbm.1_Silent_p.G330G|DBNL_uc011kbn.1_Silent_p.G251G|DBNL_uc011kbo.1_Silent_p.G255G|DBNL_uc011kbp.1_Silent_p.G306G|DBNL_uc011kbq.1_Silent_p.G279G|DBNL_uc011kbr.1_Silent_p.G303G|DBNL_uc011kbs.1_Silent_p.G259G	NM_001014436	NP_001014436	Q9UJU6	DBNL_HUMAN	drebrin-like isoform b	354					activation of JUN kinase activity|cellular component disassembly involved in apoptosis|endocytosis|Rac protein signal transduction	cell cortex|cytoskeleton|cytosol|lamellipodium	actin binding|enzyme activator activity|identical protein binding			skin(1)	1						AGCAGCAAGGTGCTGGCTCTG	0.607													4	15	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48556400	48556400	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48556400C>A	uc003toq.2	+	52	13745	c.13720C>A	c.(13720-13722)CTA>ATA	p.L4574I	ABCA13_uc010kys.1_Missense_Mutation_p.L1649I|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Missense_Mutation_p.L304I	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4574	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						CTATGTCTCACTAAACTTCAT	0.428													30	106	---	---	---	---	PASS
CLIP2	7461	broad.mit.edu	37	7	73803459	73803459	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73803459G>T	uc003uam.2	+	13	2917	c.2590G>T	c.(2590-2592)GAG>TAG	p.E864*	CLIP2_uc003uan.2_Nonsense_Mutation_p.E829*	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	864	Potential.					microtubule associated complex				skin(3)	3						TAAGTCAGGCGAGAAGAAGGT	0.627													7	36	---	---	---	---	PASS
CACNA2D1	781	broad.mit.edu	37	7	81611871	81611871	+	Intron	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81611871A>G	uc003uhr.1	-							NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	TCAAAAATACAACAAAACCAA	0.373													17	46	---	---	---	---	PASS
CACNA2D1	781	broad.mit.edu	37	7	81624184	81624184	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81624184C>T	uc003uhr.1	-	20	1990	c.1734G>A	c.(1732-1734)GAG>GAA	p.E578E		NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	597	Extracellular (Potential).					voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	CAATTCTTACCTCATCTTGAG	0.264													8	31	---	---	---	---	PASS
ABCB4	5244	broad.mit.edu	37	7	87079412	87079412	+	Intron	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87079412G>A	uc003uiv.1	-						ABCB4_uc003uiw.1_Intron|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4						cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					AGAGTATCTGGACAGAAAAGA	0.453													24	49	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94024514	94024514	+	Intron	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94024514A>G	uc003ung.1	+						COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor						axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TTCCAGGTACACTTGGAGGGC	0.453										HNSCC(75;0.22)	OREG0018169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	23	69	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94035032	94035032	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94035032C>A	uc003ung.1	+	11	1005	c.534C>A	c.(532-534)GGC>GGA	p.G178G	COL1A2_uc011kib.1_Intron|COL1A2_uc010lfh.1_RNA	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	178					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GCTTCAAAGGCATTAGGGTGA	0.363										HNSCC(75;0.22)			25	92	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94058495	94058495	+	Intron	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94058495T>C	uc003ung.1	+						COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor						axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TCCTATTTTCTGTAGTTTGAA	0.378										HNSCC(75;0.22)			11	25	---	---	---	---	PASS
CYP3A4	1576	broad.mit.edu	37	7	99381709	99381709	+	5'UTR	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99381709A>G	uc003urv.1	-	1					CYP3A4_uc003urw.1_5'UTR|CYP3A4_uc011kiz.1_5'UTR|CYP3A4_uc011kja.1_5'UTR|CYP3A4_uc011kjb.1_5'UTR	NM_017460	NP_059488	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A,						alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process	cell surface|endoplasmic reticulum membrane|integral to membrane|microsome	albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity			central_nervous_system(3)|ovary(1)	4	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)	AGCCATCACTACTTTCCTTAC	0.522													19	39	---	---	---	---	PASS
DOCK4	9732	broad.mit.edu	37	7	111462506	111462506	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111462506G>A	uc003vfx.2	-	27	3111	c.2842C>T	c.(2842-2844)CTG>TTG	p.L948L	DOCK4_uc003vfw.2_Silent_p.L389L|DOCK4_uc003vfy.2_Silent_p.L984L	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	948					cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				ATCTGCAGCAGGAAATCCTTG	0.388													9	31	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	122114483	122114483	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122114483G>A	uc010lkp.2	-	12	2113	c.1950C>T	c.(1948-1950)CTC>CTT	p.L650L	CADPS2_uc011knx.1_Silent_p.L21L|CADPS2_uc003vkg.3_Silent_p.L347L|CADPS2_uc010lkq.2_Silent_p.L647L	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	650					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						TCTGCCTCTGGAGTATTCTAA	0.383													15	61	---	---	---	---	PASS
KLHDC10	23008	broad.mit.edu	37	7	129764369	129764369	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129764369A>T	uc003vpj.1	+	6	993	c.858A>T	c.(856-858)TTA>TTT	p.L286F	KLHDC10_uc003vpk.1_Missense_Mutation_p.L257F|KLHDC10_uc010lmb.1_Missense_Mutation_p.L183F	NM_014997	NP_055812	Q6PID8	KLD10_HUMAN	kelch domain containing 10	286	Kelch 4.										0						CATATTCCTTAAACAAGGTAT	0.368													13	37	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149482226	149482226	+	Missense_Mutation	SNP	G	C	C	rs149954255	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149482226G>C	uc010lpk.2	+	21	2900	c.2900G>C	c.(2899-2901)CGC>CCC	p.R967P	SSPO_uc010lpl.1_Missense_Mutation_p.A303P	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	967					cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CAGGACGAGCGCTGTGTGCCT	0.637													11	29	---	---	---	---	PASS
TMEM176A	55365	broad.mit.edu	37	7	150500704	150500704	+	Intron	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150500704C>A	uc003whx.1	+						TMEM176B_uc003whw.3_5'Flank	NM_018487	NP_060957	Q96HP8	T176A_HUMAN	hepatocellular carcinoma-associated antigen 112							integral to membrane				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCTCCCTCCCCAGGCCCTGC	0.537													11	45	---	---	---	---	PASS
TMEM176A	55365	broad.mit.edu	37	7	150500705	150500705	+	Intron	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150500705C>T	uc003whx.1	+						TMEM176B_uc003whw.3_5'Flank	NM_018487	NP_060957	Q96HP8	T176A_HUMAN	hepatocellular carcinoma-associated antigen 112							integral to membrane				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCTCCCTCCCCAGGCCCTGCT	0.532													12	45	---	---	---	---	PASS
SLC4A2	6522	broad.mit.edu	37	7	150773153	150773153	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150773153C>T	uc003wit.3	+	22	3781	c.3525C>T	c.(3523-3525)GCC>GCT	p.A1175A	SLC4A2_uc011kve.1_Silent_p.A1166A|SLC4A2_uc003wiu.3_Silent_p.A1161A|SLC4A2_uc003wiv.3_Silent_p.A369A|uc011kvf.1_Missense_Mutation_p.G98S	NM_003040	NP_003031	P04920	B3A2_HUMAN	solute carrier family 4, anion exchanger, member	1175	Membrane (anion exchange).|Helical; (Potential).				bicarbonate transport	integral to membrane|membrane fraction	inorganic anion exchanger activity				0			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCTGCCTGGCCCTGCTCTGGG	0.657													20	39	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151962221	151962221	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151962221A>T	uc003wla.2	-	8	1305	c.1086T>A	c.(1084-1086)TGT>TGA	p.C362*		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	362	PHD-type 1.|RING-type.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		AGTGCTGACCACAAGTAGTAC	0.448			N		medulloblastoma								18	294	---	---	---	---	PASS
INTS10	55174	broad.mit.edu	37	8	19687965	19687965	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19687965G>T	uc003wzj.2	+	10	1320	c.1189G>T	c.(1189-1191)GTA>TTA	p.V397L		NM_018142	NP_060612	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	397					snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TCGTCACATTGTAGTCAATAA	0.398													20	26	---	---	---	---	PASS
INTS10	55174	broad.mit.edu	37	8	19687967	19687967	+	Silent	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19687967A>T	uc003wzj.2	+	10	1322	c.1191A>T	c.(1189-1191)GTA>GTT	p.V397V		NM_018142	NP_060612	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	397					snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		GTCACATTGTAGTCAATAAAG	0.403													19	27	---	---	---	---	PASS
STAR	6770	broad.mit.edu	37	8	38008297	38008297	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38008297A>C	uc003xkv.1	-	1	304	c.40T>G	c.(40-42)TAC>GAC	p.Y14D	STAR_uc010lwc.1_Missense_Mutation_p.Y14D	NM_001007243	NP_001007244	P49675	STAR_HUMAN	steroidogenic acute regulatory protein isoform	14					C21-steroid hormone biosynthetic process	mitochondrial intermembrane space	cholesterol transporter activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)		ATGTGTCTGTAGGAGCTCCCA	0.418													17	395	---	---	---	---	PASS
DDHD2	23259	broad.mit.edu	37	8	38105316	38105316	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38105316A>G	uc003xlb.2	+	10	1588	c.1211A>G	c.(1210-1212)GAT>GGT	p.D404G	DDHD2_uc003xlc.2_Missense_Mutation_p.D404G|DDHD2_uc011lbl.1_Missense_Mutation_p.D216G|DDHD2_uc003xld.2_Missense_Mutation_p.D23G	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1	404	SAM.				lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			GAATTCTTTGATATCTTTGAG	0.303													43	272	---	---	---	---	PASS
WHSC1L1	54904	broad.mit.edu	37	8	38205604	38205604	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38205604C>T	uc003xli.2	-	2	604	c.86G>A	c.(85-87)CGT>CAT	p.R29H	WHSC1L1_uc011lbm.1_Missense_Mutation_p.R29H|WHSC1L1_uc010lwe.2_Missense_Mutation_p.R29H|WHSC1L1_uc003xlj.2_Missense_Mutation_p.R29H	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long	29					cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			ATCCTCCTGACGGATGTTGGC	0.468			T	NUP98	AML								56	340	---	---	---	---	PASS
ADAM2	2515	broad.mit.edu	37	8	39694659	39694659	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39694659G>A	uc003xnj.2	-	2	203	c.128C>T	c.(127-129)TCG>TTG	p.S43L	ADAM2_uc003xnk.2_Missense_Mutation_p.S43L|ADAM2_uc011lck.1_Missense_Mutation_p.S43L|ADAM2_uc003xnl.2_Missense_Mutation_p.S43L	NM_001464	NP_001455	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2 proprotein	43					cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		CATTACCTGCGATTCAATTCC	0.303													11	195	---	---	---	---	PASS
PRKDC	5591	broad.mit.edu	37	8	48743256	48743256	+	Silent	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48743256G>C	uc003xqi.2	-	62	8364	c.8307C>G	c.(8305-8307)GTC>GTG	p.V2769V	PRKDC_uc003xqj.2_Silent_p.V2769V|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	2769	KIP-binding.				cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				TGTACAGAACGACCTGGGCAT	0.483								NHEJ					13	76	---	---	---	---	PASS
LYN	4067	broad.mit.edu	37	8	56866519	56866519	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56866519G>C	uc003xsk.3	+	8	1048	c.766G>C	c.(766-768)GGG>CGG	p.G256R	LYN_uc003xsl.3_Missense_Mutation_p.G235R	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene	256	Protein kinase.|ATP (By similarity).				erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)			GCTTGGCGCTGGGCAGTTTGG	0.527													17	67	---	---	---	---	PASS
CLVS1	157807	broad.mit.edu	37	8	62212665	62212665	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62212665C>A	uc003xuh.2	+	2	603	c.279C>A	c.(277-279)CTC>CTA	p.L93L	CLVS1_uc003xug.2_Silent_p.L93L|CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Silent_p.L93L	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1	93					lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5						CCTTTAGACTCCTGGCTCAGT	0.488													25	32	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77616888	77616888	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77616888C>A	uc003yav.2	+	2	952	c.565C>A	c.(565-567)CCA>ACA	p.P189T	ZFHX4_uc003yat.1_Missense_Mutation_p.P189T|ZFHX4_uc003yau.1_Missense_Mutation_p.P189T|ZFHX4_uc003yaw.1_Missense_Mutation_p.P189T	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	189						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTCGTTCTACCCACAGATCAT	0.483										HNSCC(33;0.089)			7	40	---	---	---	---	PASS
MMP16	4325	broad.mit.edu	37	8	89130996	89130996	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89130996G>T	uc003yeb.3	-	5	1086	c.804C>A	c.(802-804)TAC>TAA	p.Y268*	MMP16_uc003yec.2_Nonsense_Mutation_p.Y268*	NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	268	Extracellular (Potential).				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8						CCATGTACTGGTAAAATGGAG	0.418													38	49	---	---	---	---	PASS
RSPO2	340419	broad.mit.edu	37	8	108973048	108973048	+	Intron	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108973048A>G	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			TCTGCATCCTAAAAACAATTT	0.294													4	23	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110489571	110489571	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110489571C>A	uc003yne.2	+	53	9139	c.9035C>A	c.(9034-9036)CCT>CAT	p.P3012H		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3012	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GATTGCTTTCCTGTACATCCG	0.408										HNSCC(38;0.096)			20	60	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113304900	113304900	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113304900C>G	uc003ynu.2	-	55	8813	c.8654G>C	c.(8653-8655)AGA>ACA	p.R2885T	CSMD3_uc003yns.2_Missense_Mutation_p.R2087T|CSMD3_uc003ynt.2_Missense_Mutation_p.R2845T|CSMD3_uc011lhx.1_Missense_Mutation_p.R2716T	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2885	Extracellular (Potential).|Sushi 19.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TCCACTTGTTCTTCCATAAAT	0.418										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			19	58	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	114388957	114388957	+	Intron	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114388957G>T	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron|CSMD3_uc003ynx.3_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						CTAAGAGCCAGGATATCTACC	0.547										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			13	63	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	114388958	114388958	+	Intron	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114388958G>T	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron|CSMD3_uc003ynx.3_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TAAGAGCCAGGATATCTACCT	0.547										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			15	62	---	---	---	---	PASS
COL14A1	7373	broad.mit.edu	37	8	121259859	121259859	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121259859C>A	uc003yox.2	+	21	2752	c.2487C>A	c.(2485-2487)TCC>TCA	p.S829S	COL14A1_uc003yoy.2_Silent_p.S507S	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	829	Fibronectin type-III 7.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CAGTACCATCCTCGGGGCCCC	0.468													17	29	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139790639	139790639	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139790639C>G	uc003yvd.2	-	15	2162	c.1715G>C	c.(1714-1716)GGA>GCA	p.G572A		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	572	Pro-rich.|Gly-rich.|Collagen-like 3.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCCAGGTGGTCCTTGGGGCCC	0.552										HNSCC(7;0.00092)			13	21	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139790640	139790640	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139790640C>A	uc003yvd.2	-	15	2161	c.1714G>T	c.(1714-1716)GGA>TGA	p.G572*		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	572	Pro-rich.|Gly-rich.|Collagen-like 3.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CCAGGTGGTCCTTGGGGCCCC	0.552										HNSCC(7;0.00092)			13	21	---	---	---	---	PASS
GPR20	2843	broad.mit.edu	37	8	142367017	142367017	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142367017C>T	uc003ywf.2	-	2	1096	c.1007G>A	c.(1006-1008)GGC>GAC	p.G336D		NM_005293	NP_005284	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	336	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			upper_aerodigestive_tract(1)	1	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			GTGATGACGGCCTGAGCCCTT	0.682													7	29	---	---	---	---	PASS
CYP11B1	1584	broad.mit.edu	37	8	143961141	143961141	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143961141C>T	uc003yxi.2	-	1	96	c.89G>A	c.(88-90)CGG>CAG	p.R30Q	CYP11B1_uc003yxj.2_Missense_Mutation_p.R30Q|CYP11B1_uc010mey.2_Missense_Mutation_p.R30Q	NM_000497	NP_000488	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B,	30					aldosterone biosynthetic process|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|glucose homeostasis|immune response|regulation of blood pressure|response to stress|xenobiotic metabolic process	mitochondrial inner membrane	electron carrier activity|steroid 11-beta-monooxygenase activity			ovary(3)	3	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Mitotane(DB00648)	CCTGGGGACCCGGGCGGCTCT	0.647									Familial_Hyperaldosteronism_type_I				37	47	---	---	---	---	PASS
KIFC2	90990	broad.mit.edu	37	8	145692606	145692606	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145692606G>T	uc003zcz.2	+	4	416	c.351G>T	c.(349-351)CTG>CTT	p.L117L	CYHR1_uc003zcv.2_5'Flank|CYHR1_uc003zcw.2_5'Flank|CYHR1_uc003zcx.2_5'Flank|CYHR1_uc003zcy.2_5'Flank	NM_145754	NP_665697	Q96AC6	KIFC2_HUMAN	kinesin family member C2	117					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			ovary(2)|central_nervous_system(1)	3	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			TCCCCTCACTGTTGACAGTGA	0.662											OREG0019057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	42	43	---	---	---	---	PASS
DOCK8	81704	broad.mit.edu	37	9	464218	464218	+	Nonstop_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:464218A>T	uc003zgf.2	+	48	6411	c.6299A>T	c.(6298-6300)TAA>TTA	p.*2100L	DOCK8_uc010mgu.2_Nonstop_Mutation_p.*1402L|DOCK8_uc010mgv.2_Nonstop_Mutation_p.*2000L|DOCK8_uc003zgk.2_Nonstop_Mutation_p.*1558L	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	2100					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CAGGGCAGCTAAGAAAAGCCA	0.488													21	39	---	---	---	---	PASS
C9orf46	55848	broad.mit.edu	37	9	5431953	5431953	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5431953T>C	uc003zjc.2	-	3	229	c.25A>G	c.(25-27)ATG>GTG	p.M9V	C9orf46_uc003zjd.2_Missense_Mutation_p.M9V	NM_018465	NP_060935	Q9HBL7	CI046_HUMAN	hypothetical protein LOC55848	9						integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)		CTTTCATTCATAGATTTTGAA	0.294													4	7	---	---	---	---	PASS
CNTLN	54875	broad.mit.edu	37	9	17409420	17409420	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17409420A>G	uc003zmz.2	+	16	2768	c.2742A>G	c.(2740-2742)CAA>CAG	p.Q914Q	CNTLN_uc003zmy.2_Silent_p.Q915Q|CNTLN_uc010mio.2_Silent_p.Q594Q	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1	915						centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		GCCAAACACAAGGAAAAGAAA	0.333													42	87	---	---	---	---	PASS
UNC13B	10497	broad.mit.edu	37	9	35377549	35377549	+	Missense_Mutation	SNP	G	T	T	rs142442316	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35377549G>T	uc003zwq.2	+	15	1965	c.1673G>T	c.(1672-1674)CGA>CTA	p.R558L	UNC13B_uc003zwr.2_Missense_Mutation_p.R558L	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like	558					excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			ATGAAGATCCGAGAGCGAAAT	0.502													30	34	---	---	---	---	PASS
SEMA4D	10507	broad.mit.edu	37	9	92011737	92011737	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92011737T>C	uc004aqo.1	-	8	901	c.329A>G	c.(328-330)AAC>AGC	p.N110S	SEMA4D_uc011ltm.1_Missense_Mutation_p.N110S|SEMA4D_uc011ltn.1_RNA|SEMA4D_uc011lto.1_RNA|SEMA4D_uc004aqp.1_Missense_Mutation_p.N108S	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	110	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						CCGGATGTAGTTGAGGCACTC	0.582													4	7	---	---	---	---	PASS
ZNF169	169841	broad.mit.edu	37	9	97062614	97062614	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97062614G>T	uc004aum.1	+	5	879	c.774G>T	c.(772-774)GGG>GGT	p.G258G		NM_194320	NP_919301	Q14929	ZN169_HUMAN	zinc finger protein 169	258						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				CACACACCGGGGAGAAGCCAT	0.567													8	23	---	---	---	---	PASS
FKTN	2218	broad.mit.edu	37	9	108366570	108366570	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108366570C>T	uc004bcr.2	+	6	660	c.444C>T	c.(442-444)GAC>GAT	p.D148D	FKTN_uc011lvx.1_Silent_p.D148D|FKTN_uc004bcs.2_Silent_p.D148D|FKTN_uc011lvy.1_Silent_p.D148D|FKTN_uc010mtm.2_Silent_p.D16D	NM_001079802	NP_001073270	O75072	FKTN_HUMAN	fukutin	148	Lumenal (Potential).				muscle organ development|negative regulation of cell proliferation|negative regulation of JNK cascade|nervous system development|regulation of protein glycosylation	cis-Golgi network|endoplasmic reticulum|extracellular space|Golgi membrane|integral to membrane|nucleus	transferase activity			breast(2)|ovary(1)	3						CCCGGCTAGACGGGATAGACT	0.473													23	28	---	---	---	---	PASS
SUSD1	64420	broad.mit.edu	37	9	114904791	114904791	+	Intron	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114904791T>C	uc004bfu.2	-						SUSD1_uc010mui.2_Intron|SUSD1_uc010muj.2_Intron	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor							integral to membrane	calcium ion binding				0						TGAAAATAAATTAATGTCAAA	0.418													33	41	---	---	---	---	PASS
MED27	9442	broad.mit.edu	37	9	134955031	134955031	+	Silent	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134955031G>C	uc004cbe.1	-	1	223	c.201C>G	c.(199-201)CTC>CTG	p.L67L	MED27_uc004cbf.1_Silent_p.L67L|MED27_uc011mco.1_Silent_p.L67L|MED27_uc004cbg.3_Silent_p.L67L	NM_004269	NP_004260	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	67					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		GTACCTACTTGAGGTCCCGGT	0.642													11	31	---	---	---	---	PASS
NOTCH1	4851	broad.mit.edu	37	9	139412360	139412360	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139412360A>T	uc004chz.2	-	8	1285	c.1285T>A	c.(1285-1287)TGC>AGC	p.C429S		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	429	Extracellular (Potential).|EGF-like 11; calcium-binding (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTGTTGATGCACTTGCCCGCA	0.662			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			23	9	---	---	---	---	PASS
NOTCH1	4851	broad.mit.edu	37	9	139413085	139413085	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139413085G>A	uc004chz.2	-	6	1057	c.1057C>T	c.(1057-1059)CGT>TGT	p.R353C		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	353	Extracellular (Potential).|EGF-like 9; calcium-binding (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity	p.R353H(1)		haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GAGGCCACACGGTCATGGCAG	0.652			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			6	9	---	---	---	---	PASS
MIR126	406913	broad.mit.edu	37	9	139565062	139565062	+	RNA	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139565062A>T	hsa-mir-126|MI0000471	+			c.9A>T			EGFL7_uc004cid.2_Intron|EGFL7_uc004cif.2_Intron|EGFL7_uc004cig.2_RNA|EGFL7_uc010nbp.2_Intron|EGFL7_uc004cie.2_Intron|EGFL7_uc004cih.2_Intron																	0						TCCGCTGGCGACGGGACATTA	0.592													14	6	---	---	---	---	PASS
LARP4B	23185	broad.mit.edu	37	10	863800	863800	+	Silent	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:863800T>C	uc001ifs.1	-	14	1601	c.1560A>G	c.(1558-1560)CCA>CCG	p.P520P		NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	520							nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						ACGGAGGCTTTGGTGGCGTTG	0.562													20	31	---	---	---	---	PASS
TAF3	83860	broad.mit.edu	37	10	8051097	8051097	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8051097G>A	uc010qbd.1	+	5	2372	c.2372G>A	c.(2371-2373)AGG>AAG	p.R791K		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	791	Pro-rich.				maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						TCGCAGAACAGGCCGAAGAcc	0.299													4	7	---	---	---	---	PASS
MCM10	55388	broad.mit.edu	37	10	13214719	13214719	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13214719A>G	uc001ima.2	+	5	650	c.549A>G	c.(547-549)CTA>CTG	p.L183L	MCM10_uc001imb.2_Silent_p.L182L|MCM10_uc001imc.2_Silent_p.L182L	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	183					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						TCCCTGCGCTACCAAGAACCA	0.458													12	29	---	---	---	---	PASS
NEBL	10529	broad.mit.edu	37	10	21250653	21250653	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21250653G>C	uc001iqk.2	-	4	659	c.305C>G	c.(304-306)ACG>AGG	p.T102R		NM_213569	NP_998734	O76041	NEBL_HUMAN	nebulette non-muscle isoform	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						AGGAGTGTCCGTGACGATGCT	0.443													35	78	---	---	---	---	PASS
NRP1	8829	broad.mit.edu	37	10	33543123	33543123	+	Splice_Site	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33543123C>A	uc001iwx.3	-	6	1338	c.815_splice	c.e6-1	p.D272_splice	NRP1_uc001iwv.3_Splice_Site_p.D272_splice|NRP1_uc009xlz.2_Splice_Site_p.D272_splice|NRP1_uc001iww.3_Splice_Site_p.D91_splice|NRP1_uc001iwy.3_Splice_Site_p.D272_splice|NRP1_uc001iwz.2_Splice_Site_p.D272_splice|NRP1_uc001ixa.2_Splice_Site_p.D272_splice|NRP1_uc001ixb.1_Splice_Site_p.D272_splice|NRP1_uc001ixc.1_Splice_Site_p.D272_splice	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)	CATTTGAAATCTGAAGGGAAA	0.398													13	24	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37505199	37505199	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37505199G>C	uc001iza.1	+	32	2891	c.2792G>C	c.(2791-2793)GGA>GCA	p.G931A		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	987						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						CAACGTACAGGAAAAATGGAA	0.333													13	54	---	---	---	---	PASS
LRRC18	474354	broad.mit.edu	37	10	50121473	50121473	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50121473G>C	uc001jhd.2	-	1	808	c.728C>G	c.(727-729)CCC>CGC	p.P243R	WDFY4_uc001jha.3_Intron|LRRC18_uc001jhe.1_Missense_Mutation_p.P243R	NM_001006939	NP_001006940	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	243						cytoplasm				ovary(1)|pancreas(1)	2						CATGGAATTGGGTGAGATCAG	0.537													45	108	---	---	---	---	PASS
SLC18A3	6572	broad.mit.edu	37	10	50820151	50820151	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50820151G>C	uc001jhw.2	+	1	1805	c.1365G>C	c.(1363-1365)ATG>ATC	p.M455I	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank|CHAT_uc001jia.2_5'Flank|CHAT_uc001jhz.2_5'Flank|CHAT_uc010qgs.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	455	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(2)	2						GCCTTGGCATGGGACTGGCCA	0.637													6	23	---	---	---	---	PASS
A1CF	29974	broad.mit.edu	37	10	52573785	52573785	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52573785C>A	uc001jjj.2	-	10	1367	c.1179G>T	c.(1177-1179)GTG>GTT	p.V393V	A1CF_uc010qhn.1_Silent_p.V393V|A1CF_uc001jji.2_Silent_p.V385V|A1CF_uc001jjh.2_Silent_p.V393V|A1CF_uc010qho.1_Silent_p.V401V|A1CF_uc009xov.2_Silent_p.V385V	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	393	Required for nuclear localization.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1						CCAGTCCTCTCACTCCCGCAG	0.463													8	30	---	---	---	---	PASS
CTNNA3	29119	broad.mit.edu	37	10	67680202	67680202	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67680202C>A	uc009xpn.1	-	18	2697	c.2574G>T	c.(2572-2574)TTG>TTT	p.L858F	CTNNA3_uc001jmw.2_Missense_Mutation_p.L858F	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3	858					cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						CTCTTTTAATCAAGGGTTTTT	0.473													14	53	---	---	---	---	PASS
DYDC1	143241	broad.mit.edu	37	10	82102128	82102128	+	Intron	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82102128A>G	uc001kbx.2	-						DYDC1_uc001kby.1_Intron|DYDC1_uc009xsr.1_Intron|DYDC2_uc001kbz.1_5'Flank|DYDC2_uc001kca.1_5'Flank	NM_138812	NP_620167	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1												0			Colorectal(32;0.229)			CTGAATATTCAGAAATATGTC	0.358													17	29	---	---	---	---	PASS
RGR	5995	broad.mit.edu	37	10	86007505	86007505	+	Splice_Site	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86007505T>C	uc001kdc.1	+	2	274	c.236_splice	c.e2+2	p.R79_splice	RGR_uc001kdb.1_Splice_Site_p.P62_splice|RGR_uc001kdd.1_Splice_Site_p.R79_splice|RGR_uc001kde.1_Splice_Site_p.R79_splice	NM_001012720	NP_001012738	P47804	RGR_HUMAN	retinal G-protein coupled receptor isoform 2						phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity|protein binding			ovary(1)	1						CCTTCTCCGGTACCAGCCCCC	0.637													9	31	---	---	---	---	PASS
ZNF518A	9849	broad.mit.edu	37	10	97918053	97918053	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97918053A>G	uc001klp.2	+	6	2831	c.1974A>G	c.(1972-1974)GCA>GCG	p.A658A	ZNF518A_uc001klo.1_Silent_p.A128A|ZNF518A_uc001klq.2_Silent_p.A658A|ZNF518A_uc001klr.2_Silent_p.A658A	NM_014803	NP_055618	Q6AHZ1	Z518A_HUMAN	zinc finger protein 518	658					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		CAGGAACAGCAGTGTATGAAA	0.373													22	45	---	---	---	---	PASS
LOXL4	84171	broad.mit.edu	37	10	100010855	100010855	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100010855C>T	uc001kpa.1	-	14	2318	c.2167G>A	c.(2167-2169)GGG>AGG	p.G723R		NM_032211	NP_115587	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4 precursor	723	Lysyl-oxidase like.					extracellular space|membrane	copper ion binding|protein binding|scavenger receptor activity			ovary(3)|breast(1)|skin(1)	5		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		ACCCGGTGCCCATCATACTTG	0.522													6	14	---	---	---	---	PASS
PDZD7	79955	broad.mit.edu	37	10	102783315	102783315	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102783315G>T	uc001kso.1	-	4	635	c.420C>A	c.(418-420)AGC>AGA	p.S140R	PDZD7_uc001ksn.2_Missense_Mutation_p.S140R	NM_024895	NP_079171	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	140	PDZ 1.					cilium|nucleus	protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		TGCTCTCCAGGCTCAGCCCAT	0.657													8	21	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108337279	108337279	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108337279T>C	uc001kym.2	-	26	3414	c.3406A>G	c.(3406-3408)ACT>GCT	p.T1136A	SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_3'UTR	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	1136	Cytoplasmic (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CCAGGTTGAGTAGAAGGGGAG	0.493													23	42	---	---	---	---	PASS
PNLIPRP1	5407	broad.mit.edu	37	10	118354329	118354329	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118354329G>A	uc001lco.1	+	5	436	c.418G>A	c.(418-420)GTG>ATG	p.V140M	PNLIPRP1_uc001lcp.2_Missense_Mutation_p.V140M|PNLIPRP1_uc009xys.1_RNA	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor	140					lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)		TGCCAACAACGTGCGAGTGGT	0.602													9	17	---	---	---	---	PASS
RAB11FIP2	22841	broad.mit.edu	37	10	119805520	119805520	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119805520G>C	uc001ldj.1	-	1	595	c.155C>G	c.(154-156)GCT>GGT	p.A52G	RAB11FIP2_uc009xyz.1_Missense_Mutation_p.A52G|CASC2_uc001ldm.3_5'Flank|CASC2_uc009xzc.2_5'Flank|CASC2_uc001ldk.2_5'Flank|CASC2_uc009xza.2_5'Flank|CASC2_uc009xzb.2_5'Flank	NM_014904	NP_055719	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2	52	C2.|Necessary for its cellular translocation to the plasma membrane.				protein transport	plasma membrane|recycling endosome membrane	protein homodimerization activity				0		Colorectal(252;0.235)		all cancers(201;0.0238)		GGTTTTCTCAGCTACAGAGGT	0.448													16	35	---	---	---	---	PASS
C10orf120	399814	broad.mit.edu	37	10	124457592	124457592	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124457592T>A	uc001lgn.2	-	3	697	c.665A>T	c.(664-666)GAT>GTT	p.D222V		NM_001010912	NP_001010912	Q5SQS8	CJ120_HUMAN	hypothetical protein LOC399814	222										kidney(1)	1		all_neural(114;0.169)|Glioma(114;0.222)				TTGGTTGGCATCATCACAATT	0.398													12	23	---	---	---	---	PASS
DOCK1	1793	broad.mit.edu	37	10	129172398	129172398	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129172398A>T	uc001ljt.2	+	35	3596	c.3532A>T	c.(3532-3534)ATG>TTG	p.M1178L	DOCK1_uc010qun.1_Missense_Mutation_p.M1199L|DOCK1_uc009yaq.2_Missense_Mutation_p.M173L	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1178	DHR-2.				apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TGTGCGCTTAATGGAAAGGCT	0.423													10	17	---	---	---	---	PASS
OR51A4	401666	broad.mit.edu	37	11	4967961	4967961	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4967961T>C	uc010qys.1	-	1	370	c.370A>G	c.(370-372)AGA>GGA	p.R124G		NM_001005329	NP_001005329	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A,	124	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCTAGGAATCTATCAAATGAC	0.448													49	77	---	---	---	---	PASS
TRIM22	10346	broad.mit.edu	37	11	5719761	5719761	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5719761G>C	uc001mbr.2	+	4	1013	c.736G>C	c.(736-738)GTA>CTA	p.V246L	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Missense_Mutation_p.V214L|TRIM22_uc009yes.2_Missense_Mutation_p.V242L|TRIM22_uc010qzm.1_Missense_Mutation_p.V74L|TRIM22_uc009yeu.2_Missense_Mutation_p.V57L	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22	246	Potential.				immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		GGGATCGTCAGTAGAGATGCT	0.547													6	12	---	---	---	---	PASS
OR52L1	338751	broad.mit.edu	37	11	6007601	6007601	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6007601C>A	uc001mcd.2	-	1	615	c.560G>T	c.(559-561)TGC>TTC	p.C187F		NM_001005173	NP_001005173	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L,	187	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGTGGCTTGGCAGAAGATAAG	0.493													31	48	---	---	---	---	PASS
STK33	65975	broad.mit.edu	37	11	8479036	8479036	+	Intron	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8479036T>C	uc001mgi.1	-						STK33_uc001mgj.1_Intron|STK33_uc001mgk.1_Intron|STK33_uc010rbn.1_Intron|STK33_uc001mgl.3_Intron|STK33_uc009yfp.2_Intron	NM_030906	NP_112168	Q9BYT3	STK33_HUMAN	serine/threonine kinase 33							Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		TCTGACATTATATATATAAAA	0.308													10	22	---	---	---	---	PASS
C11orf16	56673	broad.mit.edu	37	11	8947056	8947056	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8947056C>G	uc001mhb.3	-	5	1282	c.1158G>C	c.(1156-1158)TGG>TGC	p.W386C	C11orf16_uc001mhc.3_Missense_Mutation_p.W386C	NM_020643	NP_065694	Q9NQ32	CK016_HUMAN	hypothetical protein LOC56673	386										upper_aerodigestive_tract(1)|pancreas(1)	2				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		TCCAATACCTCCACTCAGGCT	0.592													13	40	---	---	---	---	PASS
GALNTL4	374378	broad.mit.edu	37	11	11642897	11642897	+	Intron	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11642897C>A	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		GTTTCCGGGGCGCCCGTACCT	0.642													18	23	---	---	---	---	PASS
ABCC8	6833	broad.mit.edu	37	11	17464298	17464298	+	Silent	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17464298G>C	uc001mnc.2	-	10	1725	c.1599C>G	c.(1597-1599)CTC>CTG	p.L533L	ABCC8_uc010rcy.1_Silent_p.L532L	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	533	Cytoplasmic (By similarity).|ABC transmembrane type-1 1.				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	CAAAGGCCCTGAGGCTGGTCA	0.607													10	29	---	---	---	---	PASS
ANO5	203859	broad.mit.edu	37	11	22249067	22249067	+	Silent	SNP	C	A	A	rs149040903		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22249067C>A	uc001mqi.2	+	7	900	c.583C>A	c.(583-585)CGG>AGG	p.R195R	ANO5_uc001mqj.2_Silent_p.R194R	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	195	Cytoplasmic (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4						CAGCAGACATCGGCAGGAGCT	0.453													21	47	---	---	---	---	PASS
BBOX1	8424	broad.mit.edu	37	11	27148880	27148880	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27148880C>T	uc001mre.1	+	9	1412	c.1044C>T	c.(1042-1044)GGC>GGT	p.G348G	BBOX1_uc009yih.1_Silent_p.G348G|BBOX1_uc001mrg.1_Silent_p.G348G	NM_003986	NP_003977	O75936	BODG_HUMAN	gamma-butyrobetaine dioxygenase	348					carnitine biosynthetic process	actin cytoskeleton|cytosol|intracellular membrane-bounded organelle	gamma-butyrobetaine dioxygenase activity|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1					Succinic acid(DB00139)|Vitamin C(DB00126)	TACTTCATGGCCGACGTAGCT	0.408													14	28	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587801	55587801	+	Silent	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587801C>G	uc010rin.1	+	1	696	c.696C>G	c.(694-696)GTC>GTG	p.V232V		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	232	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				TGCGTTCAGTCAGTGGGCGCC	0.493													27	67	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55944513	55944513	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944513G>T	uc010rjb.1	+	1	420	c.420G>T	c.(418-420)AAG>AAT	p.K140N		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	140	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					CTGATAGAAAGTGTGTGGAGC	0.453													17	52	---	---	---	---	PASS
OR5T2	219464	broad.mit.edu	37	11	56000524	56000524	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56000524A>G	uc010rjc.1	-	1	138	c.138T>C	c.(136-138)ACT>ACC	p.T46T		NM_001004746	NP_001004746	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T,	46	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					AGGTAACTTCAGTGACATTCT	0.363													16	45	---	---	---	---	PASS
OR5M9	390162	broad.mit.edu	37	11	56230145	56230145	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56230145C>A	uc010rjj.1	-	1	733	c.733G>T	c.(733-735)GCT>TCT	p.A245S		NM_001004743	NP_001004743	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M,	245	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4	Esophageal squamous(21;0.00448)					ATAGAAACAGCCGTCAAGTGG	0.532													7	20	---	---	---	---	PASS
OR9Q2	219957	broad.mit.edu	37	11	57958617	57958617	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57958617C>G	uc010rka.1	+	1	655	c.655C>G	c.(655-657)CTG>GTG	p.L219V		NM_001005283	NP_001005283	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)|central_nervous_system(1)	4		Breast(21;0.0589)				GGTATCCTACCTGTTTATCAT	0.522													11	47	---	---	---	---	PASS
OR1S1	219959	broad.mit.edu	37	11	57982498	57982498	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57982498G>C	uc010rkc.1	+	1	282	c.282G>C	c.(280-282)ATG>ATC	p.M94I		NM_001004458	NP_001004458	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S,	94	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1		Breast(21;0.0589)				TCCCCAAAATGCTGGTGAATA	0.408													22	117	---	---	---	---	PASS
OR1S1	219959	broad.mit.edu	37	11	57982499	57982499	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57982499C>T	uc010rkc.1	+	1	283	c.283C>T	c.(283-285)CTG>TTG	p.L95L		NM_001004458	NP_001004458	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S,	95	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1		Breast(21;0.0589)				CCCCAAAATGCTGGTGAATAT	0.403													20	117	---	---	---	---	PASS
OR5B21	219968	broad.mit.edu	37	11	58274962	58274962	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58274962A>T	uc010rki.1	-	1	617	c.617T>A	c.(616-618)TTC>TAC	p.F206Y		NM_001005218	NP_001005218	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B,	206	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CAGGAGGGTGAAAAAGACGTT	0.473													12	31	---	---	---	---	PASS
DAGLA	747	broad.mit.edu	37	11	61490431	61490431	+	Silent	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61490431C>G	uc001nsa.2	+	4	519	c.408C>G	c.(406-408)CTC>CTG	p.L136L		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	136	Extracellular (Potential).				cell death|lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3				READ - Rectum adenocarcinoma(4;0.219)		ATGTCACCCTCGGTACGTCTG	0.592													14	47	---	---	---	---	PASS
FADS3	3995	broad.mit.edu	37	11	61645000	61645000	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61645000C>A	uc001nsm.2	-	7	1021	c.868G>T	c.(868-870)GTG>TTG	p.V290L	FADS3_uc001nsn.2_Missense_Mutation_p.V166L	NM_021727	NP_068373	Q9Y5Q0	FADS3_HUMAN	fatty acid desaturase 3	290	Lumenal (Potential).				electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	heme binding|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water			ovary(1)|pancreas(1)	2						TGCATGCACACCAGCATGTAC	0.637													9	24	---	---	---	---	PASS
PPP2R5B	5526	broad.mit.edu	37	11	64695280	64695280	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64695280G>A	uc001oby.2	+	4	988	c.403G>A	c.(403-405)GTG>ATG	p.V135M	PPP2R5B_uc001obz.2_Missense_Mutation_p.V135M	NM_006244	NP_006235	Q15173	2A5B_HUMAN	beta isoform of regulatory subunit B56, protein	135					signal transduction	cytoplasm|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(2)	2						TCAGATCTCAGTGAATATCTT	0.468													19	40	---	---	---	---	PASS
C11orf2	738	broad.mit.edu	37	11	64878989	64878989	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64878989C>T	uc001ocr.1	+	10	2319	c.2279C>T	c.(2278-2280)GCT>GTT	p.A760V	TM7SF2_uc001oct.2_5'Flank|TM7SF2_uc010rny.1_5'Flank|TM7SF2_uc001ocu.2_5'Flank|TM7SF2_uc001ocv.2_5'Flank|C11orf2_uc001ocs.1_Missense_Mutation_p.A636V	NM_013265	NP_037397	Q9UID3	FFR_HUMAN	chromosome 11 open reading frame 2	760					lipid transport|protein transport	Golgi apparatus|integral to membrane					0						GTGGCCTCTGCTGCCCTGCGC	0.637													13	20	---	---	---	---	PASS
TMEM134	80194	broad.mit.edu	37	11	67234994	67234994	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67234994G>C	uc001olq.1	-	3	375	c.307C>G	c.(307-309)CGC>GGC	p.R103G	TMEM134_uc001olp.1_Missense_Mutation_p.R94G|TMEM134_uc001olr.1_Missense_Mutation_p.R103G|TMEM134_uc001ols.1_RNA|TMEM134_uc001olt.1_RNA|TMEM134_uc010rpt.1_Missense_Mutation_p.R94G|TMEM134_uc009yrx.2_Missense_Mutation_p.R103G|TMEM134_uc010rpu.1_Missense_Mutation_p.S97R|TMEM134_uc001olu.3_Missense_Mutation_p.S106R	NM_025124	NP_079400	Q9H6X4	TM134_HUMAN	transmembrane protein 134 isoform a	103	Cytoplasmic (Potential).					integral to membrane					0						TTGTAGGAGCGCTGGGTGCTG	0.682													4	35	---	---	---	---	PASS
C2CD3	26005	broad.mit.edu	37	11	73785376	73785376	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73785376G>A	uc001ouu.2	-	24	5100	c.4873C>T	c.(4873-4875)CAG>TAG	p.Q1625*	C2CD3_uc001out.2_RNA	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1625	C2 2.			Q -> R (in Ref. 1; BAC86334).		centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					GGGCCCTCCTGCGTCAGGCGG	0.567													5	44	---	---	---	---	PASS
CCDC89	220388	broad.mit.edu	37	11	85397009	85397009	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85397009C>A	uc001pau.1	-	1	312	c.165G>T	c.(163-165)CTG>CTT	p.L55L		NM_152723	NP_689936	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	55	Potential.					cytoplasm|nucleus					0		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CCTCCTCTGACAGTCCCCGGA	0.547													13	40	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93826744	93826744	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93826744C>A	uc001pep.2	+	13	2529	c.2372C>A	c.(2371-2373)ACG>AAG	p.T791K	uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	791	Plastocyanin-like 5.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				AGGGAATATACGGATGGAGAA	0.463													60	99	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93836182	93836182	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93836182T>A	uc001pep.2	+	15	2835	c.2678T>A	c.(2677-2679)GTG>GAG	p.V893E	uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	893	Plastocyanin-like 5.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GTAAACTTTGTGAAGGTAAGG	0.378													8	59	---	---	---	---	PASS
CNTN5	53942	broad.mit.edu	37	11	99827644	99827644	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99827644A>T	uc001pga.2	+	8	1119	c.780A>T	c.(778-780)CAA>CAT	p.Q260H	CNTN5_uc009ywv.1_Missense_Mutation_p.Q260H|CNTN5_uc001pfz.2_Missense_Mutation_p.Q260H|CNTN5_uc001pgb.2_Missense_Mutation_p.Q186H	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	260	Ig-like C2-type 2.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		CTAAAGTCCAAACATCAGATG	0.458													20	31	---	---	---	---	PASS
ANGPTL5	253935	broad.mit.edu	37	11	101771162	101771162	+	Silent	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101771162T>C	uc001pgl.2	-	7	1256	c.660A>G	c.(658-660)CTA>CTG	p.L220L		NM_178127	NP_835228	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5 precursor	220	Fibrinogen C-terminal.				signal transduction	extracellular space	receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)		AAAATTAACCTAGAAGATCTC	0.348													19	28	---	---	---	---	PASS
ZC3H12C	85463	broad.mit.edu	37	11	110034020	110034020	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110034020C>A	uc009yxw.2	+	5	1222	c.1171C>A	c.(1171-1173)CTT>ATT	p.L391I	ZC3H12C_uc010rwc.1_Missense_Mutation_p.L392I|ZC3H12C_uc010rwd.1_Missense_Mutation_p.L392I|ZC3H12C_uc001pkr.3_Missense_Mutation_p.L360I	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	391							endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		TGATGACCCTCTTGGCAGACA	0.393													4	35	---	---	---	---	PASS
TMPRSS5	80975	broad.mit.edu	37	11	113570795	113570795	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113570795C>A	uc001poc.3	-	2	221	c.99G>T	c.(97-99)CAG>CAT	p.Q33H	TMPRSS5_uc009yys.2_5'UTR|TMPRSS5_uc009yyt.2_Intron|TMPRSS5_uc001pod.3_Intron|TMPRSS5_uc010rww.1_Missense_Mutation_p.Q23H|TMPRSS5_uc009yyu.2_Intron|TMPRSS5_uc010rwx.1_Intron	NM_030770	NP_110397	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	33	Cytoplasmic (Potential).				proteolysis	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)	1		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		TACTGGGATGCTGCTGGTCTC	0.617													3	9	---	---	---	---	PASS
CLDN25	644672	broad.mit.edu	37	11	113650742	113650742	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113650742G>C	uc009yyw.1	+	1	225	c.225G>C	c.(223-225)CAG>CAC	p.Q75H		NM_001101389	NP_001094859	C9JDP6	CLD25_HUMAN	claudin 25	75	Extracellular (Potential).					integral to membrane|tight junction	structural molecule activity				0						CTCTGCCCCAGGAGCTCCAGG	0.562													47	112	---	---	---	---	PASS
APOA4	337	broad.mit.edu	37	11	116692455	116692455	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116692455C>T	uc001pps.1	-	3	423	c.319G>A	c.(319-321)GAG>AAG	p.E107K		NM_000482	NP_000473			apolipoprotein A-IV precursor												0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		ctcagctcctccagctccttc	0.025													4	10	---	---	---	---	PASS
DSCAML1	57453	broad.mit.edu	37	11	117308664	117308664	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117308664C>T	uc001prh.1	-	25	4561	c.4559G>A	c.(4558-4560)AGC>AAC	p.S1520N		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1460	Fibronectin type-III 5.|Extracellular (Potential).				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		AGAGCCCACGCTGTTCTTGGC	0.637													9	25	---	---	---	---	PASS
CRTAM	56253	broad.mit.edu	37	11	122726575	122726575	+	Intron	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122726575C>G	uc001pyj.2	+							NM_019604	NP_062550	O95727	CRTAM_HUMAN	class-I MHC-restricted T cell associated						cell recognition|detection of tumor cell|positive regulation of cytokine secretion|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	integral to membrane|plasma membrane	receptor binding			ovary(1)	1		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GTAAGAAGAACTAATGATTCT	0.373													6	24	---	---	---	---	PASS
OR6X1	390260	broad.mit.edu	37	11	123624810	123624810	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123624810G>T	uc010rzy.1	-	1	417	c.417C>A	c.(415-417)TGC>TGA	p.C139*		NM_001005188	NP_001005188	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X,	139	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CCAGCTGCAGGCAGAGTTTGC	0.522													21	78	---	---	---	---	PASS
SLC6A13	6540	broad.mit.edu	37	12	330173	330173	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:330173C>A	uc001qic.1	-	15	1803	c.1750G>T	c.(1750-1752)GCT>TCT	p.A584S	SLC6A13_uc009zdj.1_Missense_Mutation_p.A574S|SLC6A13_uc010sdl.1_Missense_Mutation_p.A492S	NM_016615	NP_057699	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter	584	Cytoplasmic (Potential).				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GTGGCGGGAGCCGAGGGTCCT	0.657													8	11	---	---	---	---	PASS
VWF	7450	broad.mit.edu	37	12	6061009	6061009	+	Splice_Site	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6061009C>A	uc001qnn.1	-	50	8405	c.8155_splice	c.e50+1	p.C2719_splice	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	AACGCACTCACATGTGTCACA	0.448													12	28	---	---	---	---	PASS
USP5	8078	broad.mit.edu	37	12	6964980	6964980	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6964980C>T	uc001qri.3	+	3	358	c.299C>T	c.(298-300)GCT>GTT	p.A100V	USP5_uc001qrh.3_Missense_Mutation_p.A100V	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	100					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			lung(2)|breast(1)|skin(1)	4						ACGCGGCTGGCTATTGGTGAG	0.577													12	29	---	---	---	---	PASS
C1R	715	broad.mit.edu	37	12	7187955	7187955	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7187955G>A	uc010sfy.1	-	10	2058	c.1999C>T	c.(1999-2001)CGC>TGC	p.R667C		NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	667	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GCCACCCAGCGATCAGTGTTC	0.567													10	41	---	---	---	---	PASS
CLEC4C	170482	broad.mit.edu	37	12	7882298	7882298	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7882298C>A	uc001qtg.1	-	6	710	c.536G>T	c.(535-537)CGT>CTT	p.R179L	CLEC4C_uc001qth.1_Missense_Mutation_p.R179L|CLEC4C_uc001qti.1_Missense_Mutation_p.R148L	NM_130441	NP_569708	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C isoform	179	Extracellular (Potential).|C-type lectin.				innate immune response	integral to membrane	sugar binding			ovary(2)|skin(1)	3				Kidney(36;0.0915)		TATCGCACAACGCTCATCAAG	0.418													17	39	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	14019093	14019093	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14019093G>T	uc001rbt.2	-	2	229	c.50C>A	c.(49-51)GCC>GAC	p.A17D		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	17					response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GGCCAGGACGGCCAACACCAA	0.557													9	31	---	---	---	---	PASS
PLEKHA5	54477	broad.mit.edu	37	12	19473549	19473549	+	Silent	SNP	A	G	G	rs146976787		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19473549A>G	uc001reb.2	+	13	1985	c.1899A>G	c.(1897-1899)GTA>GTG	p.V633V	PLEKHA5_uc010sie.1_Silent_p.V736V|PLEKHA5_uc001rea.2_Silent_p.V691V|PLEKHA5_uc009zin.2_Silent_p.V391V|PLEKHA5_uc010sif.1_Silent_p.V564V|PLEKHA5_uc010sig.1_Silent_p.V552V|PLEKHA5_uc010sih.1_Silent_p.V525V|PLEKHA5_uc001rec.1_Silent_p.V379V|PLEKHA5_uc009zio.2_5'Flank	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A	633							1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					CTGAAGAAGTAGATATTGATG	0.308													22	67	---	---	---	---	PASS
SLCO1C1	53919	broad.mit.edu	37	12	20858991	20858991	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20858991C>G	uc001rej.3	+	5	735	c.380C>G	c.(379-381)GCA>GGA	p.A127G	SLCO1C1_uc010sii.1_Missense_Mutation_p.A127G|SLCO1C1_uc010sij.1_Missense_Mutation_p.A127G|SLCO1C1_uc009zip.2_Intron|SLCO1C1_uc001rei.2_Missense_Mutation_p.A127G|SLCO1C1_uc010sik.1_Missense_Mutation_p.A9G	NM_017435	NP_059131	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family,	127	Helical; Name=3; (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)					CTGCTCATTGCAATGCCTCAG	0.378													59	161	---	---	---	---	PASS
LDHB	3945	broad.mit.edu	37	12	21790085	21790085	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21790085T>C	uc001rfc.2	-	6	775	c.757A>G	c.(757-759)ATT>GTT	p.I253V	LDHB_uc001rfd.2_Missense_Mutation_p.I253V|LDHB_uc001rfe.2_Missense_Mutation_p.I253V	NM_002300	NP_002291	P07195	LDHB_HUMAN	L-lactate dehydrogenase B	253					glycolysis|pyruvate metabolic process	cytosol	L-lactate dehydrogenase activity			breast(2)|ovary(1)	3					NADH(DB00157)	CTTAATCCAATAGCCCAGTTG	0.323													21	46	---	---	---	---	PASS
ABCC9	10060	broad.mit.edu	37	12	21998678	21998678	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21998678G>T	uc001rfi.1	-	24	2975	c.2955C>A	c.(2953-2955)TAC>TAA	p.Y985*	ABCC9_uc001rfh.2_Nonsense_Mutation_p.Y985*|ABCC9_uc001rfj.1_Nonsense_Mutation_p.Y949*	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	985	Cytoplasmic (Potential).				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	CAGATGTCAGGTAGCGCCAGC	0.443													14	41	---	---	---	---	PASS
SLC38A1	81539	broad.mit.edu	37	12	46591839	46591839	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46591839C>T	uc001rpa.2	-	15	1385	c.1127G>A	c.(1126-1128)CGT>CAT	p.R376H	SLC38A1_uc001rpb.2_Missense_Mutation_p.R376H|SLC38A1_uc001rpc.2_Missense_Mutation_p.R376H|SLC38A1_uc001rpd.2_Missense_Mutation_p.R376H|SLC38A1_uc001rpe.2_Missense_Mutation_p.R376H|SLC38A1_uc009zkj.1_Missense_Mutation_p.R376H	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	376	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			TAAAGATGAACGAACCTGCAA	0.373													16	33	---	---	---	---	PASS
AQP6	363	broad.mit.edu	37	12	50367133	50367133	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50367133C>T	uc001rvr.1	+	1	514	c.177C>T	c.(175-177)GCC>GCT	p.A59A	AQP6_uc001rvp.1_Intron|AQP6_uc001rvq.1_RNA	NM_001652	NP_001643	Q13520	AQP6_HUMAN	aquaporin 6	59	Helical; (Potential).				excretion|odontogenesis	integral to plasma membrane|transport vesicle membrane	anion channel activity|water channel activity				0						TACAGATTGCCATCACCTTCA	0.637													17	70	---	---	---	---	PASS
POU6F1	5463	broad.mit.edu	37	12	51584140	51584140	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51584140C>T	uc001rxy.2	-	5	988	c.796G>A	c.(796-798)GAA>AAA	p.E266K	POU6F1_uc001rxz.2_Missense_Mutation_p.E266K|POU6F1_uc001rya.2_Missense_Mutation_p.E266K	NM_002702	NP_002693	Q14863	PO6F1_HUMAN	POU class 6 homeobox 1	266	Homeobox.				brain development|heart development|muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1						TTAGCAATTTCAGTGATCTCC	0.547													28	54	---	---	---	---	PASS
KRT5	3852	broad.mit.edu	37	12	52914004	52914004	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52914004G>A	uc001san.2	-	1	240	c.77C>T	c.(76-78)TCT>TTT	p.S26F	KRT5_uc009zmh.2_Missense_Mutation_p.S26F	NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5	26	Head.				epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCGGGAGACAGACGGGGTGAT	0.662													12	21	---	---	---	---	PASS
OR10A7	121364	broad.mit.edu	37	12	55614955	55614955	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55614955C>A	uc010spf.1	+	1	147	c.147C>A	c.(145-147)ACC>ACA	p.T49T		NM_001005280	NP_001005280	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A,	49	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4						TCACAGTTACCAGTGTGGATC	0.393													58	158	---	---	---	---	PASS
ITGA7	3679	broad.mit.edu	37	12	56091005	56091005	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56091005G>T	uc001shh.2	-	11	1794	c.1574C>A	c.(1573-1575)ACT>AAT	p.T525N	ITGA7_uc001shg.2_Missense_Mutation_p.T521N|ITGA7_uc010sps.1_Missense_Mutation_p.T428N|ITGA7_uc009znw.2_5'Flank|ITGA7_uc009znx.2_Missense_Mutation_p.T408N	NM_001144996	NP_001138468	Q13683	ITA7_HUMAN	integrin alpha 7 isoform 1 precursor	565	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape	integrin complex	receptor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5						CTCACCCACAGTAGGGCTATA	0.607													7	11	---	---	---	---	PASS
DDIT3	1649	broad.mit.edu	37	12	57910715	57910715	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57910715C>T	uc001soi.2	-	4	567	c.387G>A	c.(385-387)AGG>AGA	p.R129R	MARS_uc001sof.1_Intron|DDIT3_uc009zps.2_Silent_p.R152R|DDIT3_uc009zpt.2_Silent_p.R152R	NM_004083	NP_004074	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	129					cell cycle arrest|cell redox homeostasis|mRNA transcription from RNA polymerase II promoter|negative regulation of determination of dorsal identity|regulation of DNA-dependent transcription in response to stress|response to DNA damage stimulus	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription factor binding		FUS/DDIT3(623)|EWSR1/DDIT3(43)	soft_tissue(666)|large_intestine(1)|central_nervous_system(1)|lung(1)|skin(1)|ovary(1)	671						GTGCCACTTTCCTTTCATTCT	0.542			T	FUS	liposarcoma								26	92	---	---	---	---	PASS
KIF5A	3798	broad.mit.edu	37	12	57966467	57966467	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57966467G>T	uc001sor.1	+	15	1882	c.1674G>T	c.(1672-1674)CTG>CTT	p.L558L	KIF5A_uc010srr.1_Silent_p.L469L	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	558					blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3						TGAAGGATCTGAGCGAGTTCA	0.552													29	80	---	---	---	---	PASS
OS9	10956	broad.mit.edu	37	12	58111934	58111934	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58111934G>T	uc001spj.2	+	11	1199	c.1140G>T	c.(1138-1140)AAG>AAT	p.K380N	OS9_uc010srx.1_Missense_Mutation_p.K174N|OS9_uc001spk.2_Missense_Mutation_p.K380N|OS9_uc001spl.2_Missense_Mutation_p.K380N|OS9_uc001spm.2_Missense_Mutation_p.K380N|OS9_uc001spn.2_Missense_Mutation_p.K381N|OS9_uc010sry.1_Missense_Mutation_p.K348N|OS9_uc010srz.1_Missense_Mutation_p.K321N	NM_006812	NP_006803	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum	380					ER-associated protein catabolic process|protein retention in ER lumen|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to endoplasmic reticulum stress	endoplasmic reticulum lumen|Hrd1p ubiquitin ligase complex	glycoprotein binding|protein binding|sugar binding			ovary(1)	1	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			CCCAGGGGAAGCCAAATATAG	0.527													5	20	---	---	---	---	PASS
METTL1	4234	broad.mit.edu	37	12	58165941	58165941	+	5'Flank	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58165941T>A	uc010ssd.1	-						METTL1_uc009zqc.2_5'Flank|FAM119B_uc001sqf.2_5'Flank|FAM119B_uc001sqg.2_5'Flank|FAM119B_uc009zqd.2_5'Flank	NM_005371	NP_005362	Q9UBP6	TRMB_HUMAN	methyltransferase-like protein 1 isoform a							cytoplasm|nucleus	protein binding|tRNA (guanine-N7-)-methyltransferase activity|tRNA binding				0	all_cancers(7;6.73e-81)|Lung NSC(6;1.07e-25)|all_lung(6;8.25e-24)|all_epithelial(6;4.6e-17)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.211)			GACGCAGCCATGCGCGTTGGT	0.463													8	19	---	---	---	---	PASS
PPFIA2	8499	broad.mit.edu	37	12	81688782	81688782	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81688782T>A	uc001szo.1	-	24	2918	c.2757A>T	c.(2755-2757)GCA>GCT	p.A919A	PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_RNA|PPFIA2_uc010suh.1_RNA|PPFIA2_uc010sui.1_RNA|PPFIA2_uc010suj.1_RNA|PPFIA2_uc009zsi.1_RNA|PPFIA2_uc010suf.1_RNA|PPFIA2_uc009zsh.2_RNA	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2	845										ovary(3)|lung(2)|pancreas(1)	6						CTCGGCAGGCTGCCACGTACC	0.378													4	17	---	---	---	---	PASS
UHRF1BP1L	23074	broad.mit.edu	37	12	100433461	100433461	+	Silent	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100433461C>G	uc001tgq.2	-	20	4417	c.4188G>C	c.(4186-4188)ACG>ACC	p.T1396T	UHRF1BP1L_uc001tgp.2_Silent_p.T1046T	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	1396										ovary(2)	2						GAGTGGCTTGCGTGACACTGC	0.458													12	23	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104089339	104089339	+	Silent	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104089339A>T	uc001tjw.2	+	32	3573	c.3387A>T	c.(3385-3387)CCA>CCT	p.P1129P		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1129	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						TGCTGGTCCCACAAAGACGTC	0.468													18	43	---	---	---	---	PASS
HCFC2	29915	broad.mit.edu	37	12	104489180	104489180	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104489180T>G	uc001tkj.3	+	11	1608	c.1505T>G	c.(1504-1506)CTG>CGG	p.L502R	HCFC2_uc009zul.2_RNA	NM_013320	NP_037452	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	502					regulation of transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus	transcription coactivator activity			ovary(2)|central_nervous_system(1)	3						AGTAGTTGCCTGGATGTAAGA	0.368													11	25	---	---	---	---	PASS
SART3	9733	broad.mit.edu	37	12	108920092	108920092	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108920092C>T	uc001tmz.1	-	16	2389	c.2154G>A	c.(2152-2154)CCG>CCA	p.P718P	SART3_uc001tmy.1_Silent_p.P244P|SART3_uc009zux.1_Silent_p.P330P|SART3_uc010swx.1_Silent_p.P682P|SART3_uc010swy.1_Silent_p.P604P|SART3_uc010swz.1_Missense_Mutation_p.G717R	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	718	RRM 1.				RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1						GCTTCGTGTCCGGCTCCTGCA	0.602									Porokeratosis				10	26	---	---	---	---	PASS
MED13L	23389	broad.mit.edu	37	12	116446238	116446238	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116446238C>A	uc001tvw.2	-	10	2035	c.1980G>T	c.(1978-1980)ATG>ATT	p.M660I		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	660					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		AGTTTACCTCCATTTTGGCAT	0.542													5	33	---	---	---	---	PASS
CIT	11113	broad.mit.edu	37	12	120262966	120262966	+	Intron	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120262966T>C	uc001txi.1	-						CIT_uc001txj.1_Intron	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		AAGGACTCTTTACCTGGAAAT	0.338													7	28	---	---	---	---	PASS
GLT1D1	144423	broad.mit.edu	37	12	129467608	129467608	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129467608G>T	uc010tbh.1	+	13	1038	c.1029G>T	c.(1027-1029)AGG>AGT	p.R343S	GLT1D1_uc001uhx.1_Missense_Mutation_p.R258S|GLT1D1_uc001uhy.1_RNA	NM_144669	NP_653270	Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	338					biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		AGCTCATCAGGAAGCTGGAAG	0.498													39	101	---	---	---	---	PASS
ZNF268	10795	broad.mit.edu	37	12	133779072	133779072	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133779072A>G	uc010tcf.1	+	6	1130	c.800A>G	c.(799-801)CAA>CGA	p.Q267R	ZNF268_uc010tbv.1_Missense_Mutation_p.Q106R|ZNF268_uc010tbw.1_Missense_Mutation_p.Q106R|ZNF268_uc010tbx.1_Missense_Mutation_p.Q127R|ZNF268_uc010tby.1_Missense_Mutation_p.Q106R|ZNF268_uc010tbz.1_Missense_Mutation_p.Q106R|ZNF268_uc010tca.1_Missense_Mutation_p.Q106R|ZNF268_uc010tcb.1_Missense_Mutation_p.Q127R|ZNF268_uc010tcc.1_Missense_Mutation_p.Q106R|ZNF268_uc010tcd.1_Missense_Mutation_p.Q106R|ZNF268_uc010tce.1_Missense_Mutation_p.Q106R|ZNF268_uc010tcg.1_Missense_Mutation_p.Q106R|ZNF268_uc010tch.1_Missense_Mutation_p.Q267R	NM_003415	NP_003406	Q14587	ZN268_HUMAN	zinc finger protein 268 isoform a	267						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CTTATGTGCCAACAAATGTAT	0.388													7	14	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20039417	20039417	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20039417G>A	uc001umd.2	-	10	865	c.654C>T	c.(652-654)GAC>GAT	p.D218D	TPTE2_uc009zzk.2_RNA|TPTE2_uc009zzl.2_Silent_p.D107D|TPTE2_uc001ume.2_Silent_p.D141D|TPTE2_uc009zzm.2_5'UTR|TPTE2_uc010tcm.1_RNA	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	218	Phosphatase tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TGAGGTCTAGGTCAAATCCAT	0.313													29	114	---	---	---	---	PASS
PSPC1	55269	broad.mit.edu	37	13	20346607	20346607	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20346607C>A	uc001uml.2	-	2	635	c.449G>T	c.(448-450)CGC>CTC	p.R150L	PSPC1_uc001umj.1_RNA|PSPC1_uc001umk.1_RNA	NM_001042414	NP_001035879	Q8WXF1	PSPC1_HUMAN	paraspeckle protein 1	150	RRM 1.|Sufficient for paraspeckles localization.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		TGTAGCGAAGCGAATCCGTAG	0.458													21	60	---	---	---	---	PASS
IFT88	8100	broad.mit.edu	37	13	21163944	21163944	+	Intron	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21163944C>G	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron	NM_175605	NP_783195	Q13099	IFT88_HUMAN	intraflagellar transport 88 homolog isoform 1						cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		CTTTTTCCTCCCCAAGATAAC	0.308													8	30	---	---	---	---	PASS
SPG20	23111	broad.mit.edu	37	13	36909559	36909559	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36909559G>A	uc001uvn.2	-	3	679	c.409C>T	c.(409-411)CAG>TAG	p.Q137*	SPG20_uc010ten.1_Nonsense_Mutation_p.Q137*|SPG20_uc001uvm.2_Nonsense_Mutation_p.Q137*|SPG20_uc001uvo.2_Nonsense_Mutation_p.Q137*|SPG20_uc001uvq.2_Nonsense_Mutation_p.Q137*|SPG20_uc001uvp.2_Nonsense_Mutation_p.Q137*	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	137					cell death	cytoplasm	ubiquitin protein ligase binding				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		TCAGCATGCTGAGGAGCTGAA	0.458													10	22	---	---	---	---	PASS
POSTN	10631	broad.mit.edu	37	13	38145587	38145587	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38145587G>T	uc001uwo.3	-	18	2216	c.2098C>A	c.(2098-2100)CTA>ATA	p.L700I	POSTN_uc010tet.1_Missense_Mutation_p.L201I|POSTN_uc001uwp.3_Intron|POSTN_uc001uwr.2_Missense_Mutation_p.L673I|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Missense_Mutation_p.L673I|POSTN_uc010tev.1_Intron|POSTN_uc010tew.1_Intron	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	700					cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		ACTTTTGTTAGTGTGGGTCCT	0.363													15	48	---	---	---	---	PASS
PCDH17	27253	broad.mit.edu	37	13	58208897	58208897	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58208897T>A	uc001vhq.1	+	1	3109	c.2217T>A	c.(2215-2217)ACT>ACA	p.T739T	PCDH17_uc010aec.1_Silent_p.T739T	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	739	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		AGATCCGCACTTACAACTGCC	0.557													7	34	---	---	---	---	PASS
PCDH9	5101	broad.mit.edu	37	13	67799735	67799735	+	Silent	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67799735A>T	uc001vik.2	-	2	3530	c.2838T>A	c.(2836-2838)CCT>CCA	p.P946P	PCDH9_uc001vil.2_Silent_p.P946P|PCDH9_uc010thl.1_Silent_p.P946P|PCDH9_uc001vin.3_Silent_p.P946P	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	946	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GATGAAAAGCAGGCTGTGGAG	0.498													22	63	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77670488	77670488	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77670488C>G	uc001vkf.2	-	58	9890	c.9799G>C	c.(9799-9801)GAA>CAA	p.E3267Q	MYCBP2_uc010aev.2_Missense_Mutation_p.E2671Q	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3267					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AGGTATTTTTCTCTACAGCGA	0.413													22	63	---	---	---	---	PASS
POU4F1	5457	broad.mit.edu	37	13	79175661	79175661	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79175661C>A	uc001vkv.2	-	2	1383	c.1149G>T	c.(1147-1149)GAG>GAT	p.E383D	uc001vku.1_Intron	NM_006237	NP_006228	Q01851	PO4F1_HUMAN	POU domain, class 4, transcription factor 1	383	Homeobox.				axonogenesis|regulation of transcription from RNA polymerase II promoter|synapse assembly	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		CGGCGATCTTCTCGGACGAGG	0.612													13	35	---	---	---	---	PASS
GPR18	2841	broad.mit.edu	37	13	99907653	99907653	+	Silent	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99907653C>G	uc001voe.3	-	3	975	c.474G>C	c.(472-474)CTG>CTC	p.L158L	UBAC2_uc001voa.3_Intron|UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron|GPR18_uc010afv.2_Silent_p.L158L	NM_005292	NP_005283	Q14330	GPR18_HUMAN	G protein-coupled receptor 18	158	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled				0	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	CTTTATAGAGCAGTAGCAGAG	0.507													14	40	---	---	---	---	PASS
FAM155A	728215	broad.mit.edu	37	13	108518418	108518418	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108518418G>A	uc001vql.2	-	1	1043	c.527C>T	c.(526-528)GCG>GTG	p.A176V		NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	176						integral to membrane	binding			skin(1)	1						GCCCGAGGACGCGCCCTGGGG	0.677													16	26	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111077187	111077187	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111077187C>T	uc001vqx.2	+	5	576	c.287C>T	c.(286-288)CCC>CTC	p.P96L		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	96					angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			AGGGGAGCCCCCGGAGTAACG	0.612													11	40	---	---	---	---	PASS
OR4N2	390429	broad.mit.edu	37	14	20296217	20296217	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20296217G>T	uc010tkv.1	+	1	610	c.610G>T	c.(610-612)GGC>TGC	p.G204C		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTTCAACAGTGGCCTGATGAC	0.517													19	60	---	---	---	---	PASS
OR4N2	390429	broad.mit.edu	37	14	20296218	20296218	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20296218G>T	uc010tkv.1	+	1	611	c.611G>T	c.(610-612)GGC>GTC	p.G204V		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTCAACAGTGGCCTGATGACA	0.517													19	59	---	---	---	---	PASS
FLJ10357	55701	broad.mit.edu	37	14	21547127	21547127	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21547127G>T	uc001vzp.2	+	11	2360	c.2331G>T	c.(2329-2331)GTG>GTT	p.V777V	FLJ10357_uc001vzo.1_5'UTR|FLJ10357_uc010aij.2_RNA|FLJ10357_uc010tln.1_Silent_p.V63V	NM_018071	NP_060541	Q8TER5	ARH40_HUMAN	hypothetical protein LOC55701	777					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;5.79e-11)|Epithelial(56;8.35e-09)|all cancers(55;4.23e-08)	GBM - Glioblastoma multiforme(265;0.0197)		ACCTGCACGTGCAGCAGCAAG	0.632													13	10	---	---	---	---	PASS
MYH6	4624	broad.mit.edu	37	14	23873577	23873577	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23873577G>A	uc001wjv.2	-	8	730	c.663C>T	c.(661-663)ATC>ATT	p.I221I	MYH6_uc010akp.1_Silent_p.I221I	NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	221	Myosin head-like.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TGGCCTGGATGATCTGGTCCT	0.612													30	51	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44974630	44974630	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44974630C>A	uc001wvn.2	-	1	1870	c.1561G>T	c.(1561-1563)GCC>TCC	p.A521S		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	521	Ala-rich.					cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		TCAGCAGAGGCCTCTTCTGCA	0.502													5	17	---	---	---	---	PASS
FAM179B	23116	broad.mit.edu	37	14	45468664	45468664	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45468664C>G	uc001wvv.2	+	3	2511	c.2302C>G	c.(2302-2304)CAA>GAA	p.Q768E	FAM179B_uc001wvw.2_Missense_Mutation_p.Q768E|FAM179B_uc010anc.2_RNA|FAM179B_uc001wvu.2_Missense_Mutation_p.Q768E	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	768							binding			skin(2)|upper_aerodigestive_tract(1)	3						TTCTGACTTACAATTCCTAGG	0.368													16	26	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60072126	60072126	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60072126C>A	uc001xen.1	-	5	2281	c.2072G>T	c.(2071-2073)AGG>ATG	p.R691M	RTN1_uc001xem.1_Missense_Mutation_p.R271M|RTN1_uc001xek.1_Missense_Mutation_p.R123M|RTN1_uc001xel.1_RNA|RTN1_uc010apl.1_Missense_Mutation_p.R108M	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	691	Reticulon.				neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GAAGAGCCTCCTCAGTTCCTT	0.463													15	25	---	---	---	---	PASS
C14orf135	64430	broad.mit.edu	37	14	60591742	60591742	+	Silent	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60591742A>G	uc001xer.3	+	8	2673	c.2151A>G	c.(2149-2151)GAA>GAG	p.E717E	C14orf135_uc001xeq.2_Silent_p.E717E|C14orf135_uc010apm.2_RNA	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2	951						integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		ATCATTCAGAAGAGAAGGCCT	0.358													22	38	---	---	---	---	PASS
ACTN1	87	broad.mit.edu	37	14	69341639	69341639	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69341639G>T	uc001xkl.2	-	21	2926	c.2616C>A	c.(2614-2616)TCC>TCA	p.S872S	ACTN1_uc001xkk.2_Silent_p.S468S|ACTN1_uc010ttb.1_Silent_p.S802S|ACTN1_uc001xkm.2_Silent_p.S894S|ACTN1_uc001xkn.2_Silent_p.S867S	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b	872					focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		CACCTGGCACGGAGTCGGGGC	0.667													3	14	---	---	---	---	PASS
C14orf178	283579	broad.mit.edu	37	14	78234794	78234794	+	Splice_Site	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78234794G>T	uc001xug.1	+	3	533	c.75_splice	c.e3-1	p.W25_splice	C14orf178_uc001xuh.1_Intron	NM_174943	NP_777603	Q8N769	CN178_HUMAN	hypothetical protein LOC283579											ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0273)		attttttaCAGGCATGATCAA	0.303													5	55	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94079210	94079210	+	Silent	SNP	C	T	T	rs149617798	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94079210C>T	uc001ybv.1	+	25	3440	c.3357C>T	c.(3355-3357)CAC>CAT	p.H1119H	KIAA1409_uc001ybs.1_Silent_p.H1097H	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1274						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		GGATCGACCACCAGACAGTTC	0.522													25	73	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96758029	96758029	+	Intron	SNP	T	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96758029T>G	uc001yfi.2	-							NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B											ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		CCTTCAAAATTAAAAAAGGCC	0.348													15	63	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96773242	96773242	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96773242C>T	uc001yfi.2	-	30	4680	c.4315G>A	c.(4315-4317)GAA>AAA	p.E1439K		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1439										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TGAGATTTTTCATCCAAAACA	0.343													16	16	---	---	---	---	PASS
MIR889	100126345	broad.mit.edu	37	14	101514235	101514235	+	5'Flank	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101514235T>C	hsa-mir-889|MI0005540	+						MIR544_hsa-mir-544|MI0003515_5'Flank|MIR655_hsa-mir-655|MI0003677_5'Flank																	0						GCACAGTTCTTTGGTGCTTAA	0.398													3	11	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105408092	105408092	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105408092C>T	uc010axc.1	-	7	13816	c.13696G>A	c.(13696-13698)GTG>ATG	p.V4566M	AHNAK2_uc001ypx.2_Missense_Mutation_p.V4466M	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4566						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TTGACGTCCACCTGGGGGCCC	0.627													45	145	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105408109	105408109	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105408109T>G	uc010axc.1	-	7	13799	c.13679A>C	c.(13678-13680)GAC>GCC	p.D4560A	AHNAK2_uc001ypx.2_Missense_Mutation_p.D4460A	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4560						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCCCTTGAGGTCCACTTTGGG	0.617													23	157	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105415986	105415986	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105415986G>A	uc010axc.1	-	7	5922	c.5802C>T	c.(5800-5802)GAC>GAT	p.D1934D	AHNAK2_uc001ypx.2_Silent_p.D1834D	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1934						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCCTTTCAGGTCCAGCTTGG	0.597													136	147	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105416541	105416541	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105416541C>G	uc010axc.1	-	7	5367	c.5247G>C	c.(5245-5247)TTG>TTC	p.L1749F	AHNAK2_uc001ypx.2_Missense_Mutation_p.L1649F	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1749						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGCATCTTCAAACTGGGCA	0.652													10	233	---	---	---	---	PASS
SNORD116-4	100033416	broad.mit.edu	37	15	25324300	25324300	+	Intron	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25324300G>A	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-14_uc001yxx.2_5'Flank|SNORD116-28_uc001yxy.2_5'Flank|SNORD116-15_uc001yxz.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						GAGGTCCACCGGGGGCTATAG	0.458													13	64	---	---	---	---	PASS
SNORD116-4	100033416	broad.mit.edu	37	15	25342839	25342839	+	Intron	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25342839A>T	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-28_uc001yxy.2_Intron|IPW_uc001yyb.3_Intron|uc001yyd.2_Intron|SNORD116-25_uc001yyk.2_RNA|SNORD116-26_uc001yyl.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						AATGGATCTCATCGGAATCTG	0.478													18	49	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28478864	28478864	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28478864C>A	uc001zbj.2	-	28	4403	c.4297G>T	c.(4297-4299)GTG>TTG	p.V1433L		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1433					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		ACCTCTTCCACGGGATGCTCG	0.458													15	61	---	---	---	---	PASS
GPR176	11245	broad.mit.edu	37	15	40094083	40094083	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40094083G>A	uc001zkj.1	-	3	1664	c.798C>T	c.(796-798)GCC>GCT	p.A266A	GPR176_uc010uck.1_Silent_p.A206A	NM_007223	NP_009154	Q14439	GP176_HUMAN	G protein-coupled receptor 176	266	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		AGAGCAGGGTGGCGTGCAGCT	0.582											OREG0023053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	43	---	---	---	---	PASS
MAPKBP1	23005	broad.mit.edu	37	15	42106796	42106796	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42106796C>T	uc001zok.3	+	11	1333	c.1047C>T	c.(1045-1047)GCC>GCT	p.A349A	MAPKBP1_uc001zoj.3_Silent_p.A343A|MAPKBP1_uc010bcj.2_Intron|MAPKBP1_uc010bci.2_Silent_p.A343A|MAPKBP1_uc010udb.1_Silent_p.A231A|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_Intron	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	349	WD 5.									central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		ACACCATTGCCTTGACCTTTG	0.498													31	56	---	---	---	---	PASS
ZFP106	64397	broad.mit.edu	37	15	42742430	42742430	+	Silent	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42742430T>C	uc001zpw.2	-	2	2306	c.1971A>G	c.(1969-1971)ACA>ACG	p.T657T	ZFP106_uc001zpu.2_5'Flank|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_Silent_p.T440T|ZFP106_uc001zpy.1_Silent_p.T680T	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	657						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)		TGGCTGCAGATGTCATTTGTA	0.423													32	74	---	---	---	---	PASS
SNAP23	8773	broad.mit.edu	37	15	42805639	42805639	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42805639C>A	uc001zpz.1	+	4	233	c.142C>A	c.(142-144)CAA>AAA	p.Q48K	SNAP23_uc001zqa.1_Missense_Mutation_p.Q48K	NM_003825	NP_003816	O00161	SNP23_HUMAN	synaptosomal-associated protein 23 isoform	48	t-SNARE coiled-coil homology 1.				cellular membrane fusion|post-Golgi vesicle-mediated transport|protein transport|vesicle targeting	azurophil granule|cell junction|Golgi apparatus|nucleus|plasma membrane enriched fraction|specific granule|synapse|synaptosome	protein binding				0		all_cancers(109;7.14e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;1.18e-08)|all_lung(180;4.2e-08)|Melanoma(134;0.0179)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;2.62e-06)		GCTGGATGAACAAAAGGGTAA	0.378													15	36	---	---	---	---	PASS
SLC24A5	283652	broad.mit.edu	37	15	48429046	48429046	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48429046G>A	uc001zwe.2	+	6	830	c.757G>A	c.(757-759)GAA>AAA	p.E253K	SLC24A5_uc010bel.2_Missense_Mutation_p.E193K|uc001zwf.1_5'Flank	NM_205850	NP_995322	Q71RS6	NCKX5_HUMAN	solute carrier family 24, member 5 precursor	253	Cytoplasmic (Potential).				response to stimulus	integral to membrane|melanosome|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity				0		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		CTGGGAAGATGAAGGTCAACC	0.413													12	26	---	---	---	---	PASS
C15orf33	196951	broad.mit.edu	37	15	49833966	49833966	+	Missense_Mutation	SNP	G	A	A	rs148925050		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49833966G>A	uc001zxl.2	-	10	1079	c.785C>T	c.(784-786)ACG>ATG	p.T262M	C15orf33_uc001zxm.2_Missense_Mutation_p.T228M	NM_152647	NP_689860	Q96M60	CO033_HUMAN	hypothetical protein LOC196951	262										ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)		TTCATGGAACGTTGCATATAT	0.274													21	60	---	---	---	---	PASS
THSD4	79875	broad.mit.edu	37	15	72039276	72039276	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72039276G>A	uc002atb.1	+	12	2215	c.2136G>A	c.(2134-2136)CTG>CTA	p.L712L	THSD4_uc002ate.2_Silent_p.L352L	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	712	TSP type-1 2.					proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						ACCGCAGCCTGACGGTGCAGC	0.642													7	12	---	---	---	---	PASS
CCDC33	80125	broad.mit.edu	37	15	74554868	74554868	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74554868G>A	uc002axo.2	+	3	667	c.273G>A	c.(271-273)GGG>GGA	p.G91G		NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1	294	C2.						protein binding			ovary(3)|skin(2)	5						CTATCTGGGGGGACACGGTGA	0.582													11	13	---	---	---	---	PASS
ARNT2	9915	broad.mit.edu	37	15	80806740	80806740	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80806740C>A	uc002bfr.2	+	8	1037	c.871C>A	c.(871-873)CCA>ACA	p.P291T	ARNT2_uc010unm.1_Missense_Mutation_p.P280T|ARNT2_uc002bfs.2_Missense_Mutation_p.P280T	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator	291					central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			GGCCTGGCCACCAGCAGGTAA	0.478													86	96	---	---	---	---	PASS
AP3B2	8120	broad.mit.edu	37	15	83333598	83333598	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83333598G>A	uc010uoh.1	-	17	2246	c.2069C>T	c.(2068-2070)TCC>TTC	p.S690F	AP3B2_uc010uoi.1_Missense_Mutation_p.S709F|AP3B2_uc010uoj.1_Missense_Mutation_p.S658F|AP3B2_uc010bmp.2_5'Flank|AP3B2_uc010uog.1_Missense_Mutation_p.S326F|AP3B2_uc002biy.1_5'Flank	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	690	Glu/Ser-rich.				endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)			ACTGTCTGCGGACTCCGTGGG	0.532													7	6	---	---	---	---	PASS
BNC1	646	broad.mit.edu	37	15	83926867	83926867	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83926867T>C	uc002bjt.1	-	5	2400	c.2312A>G	c.(2311-2313)AAC>AGC	p.N771S	BNC1_uc010uos.1_Missense_Mutation_p.N759S	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	771	C2H2-type 4.				epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						GAGGTTTAGGTTTGAGCTGTG	0.443													12	62	---	---	---	---	PASS
WDR93	56964	broad.mit.edu	37	15	90255313	90255313	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90255313C>A	uc002boj.2	+	5	719	c.618C>A	c.(616-618)GAC>GAA	p.D206E	WDR93_uc010bnr.2_Missense_Mutation_p.D206E	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	206					electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			AAGGAGGGGACTTTGCAGCCT	0.418													13	36	---	---	---	---	PASS
VPS33B	26276	broad.mit.edu	37	15	91543209	91543209	+	Intron	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91543209G>T	uc002bqp.1	-						VPS33B_uc002bqq.1_Intron|VPS33B_uc010uqu.1_Intron	NM_018668	NP_061138	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33B (yeast homolog))						cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(2)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					CTAGCACCTGGGAAGGTGTAA	0.507													7	127	---	---	---	---	PASS
SNRPA1	6627	broad.mit.edu	37	15	101832213	101832213	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101832213G>A	uc002bww.2	-	3	340	c.263C>T	c.(262-264)CCC>CTC	p.P88L	SNRPA1_uc002bwx.2_Intron|SNRPA1_uc010bpc.2_Intron	NM_003090	NP_003081	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	88						catalytic step 2 spliceosome|nucleoplasm|U2 snRNP	protein binding|RNA binding			kidney(1)	1	Lung NSC(78;0.00156)|all_lung(78;0.00195)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00113)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGTCAGACAGGGCAGAGCCTG	0.383													54	190	---	---	---	---	PASS
TARSL2	123283	broad.mit.edu	37	15	102261405	102261405	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102261405C>A	uc002bxm.2	-	3	545	c.490G>T	c.(490-492)GTA>TTA	p.V164L	TARSL2_uc010usi.1_RNA	NM_152334	NP_689547	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	164					threonyl-tRNA aminoacylation	cytoplasm	ATP binding|threonine-tRNA ligase activity			ovary(2)	2	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GCCACTCTTACTGTGATGATG	0.413													71	85	---	---	---	---	PASS
OR4F6	390648	broad.mit.edu	37	15	102346577	102346577	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102346577A>G	uc010utr.1	+	1	655	c.655A>G	c.(655-657)ATC>GTC	p.I219V		NM_001005326	NP_001005326	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F,	219	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			AATCTCTTACATCTTTATTTT	0.378													35	61	---	---	---	---	PASS
NARFL	64428	broad.mit.edu	37	16	789680	789680	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:789680C>T	uc002cjr.2	-	2	137	c.125G>A	c.(124-126)CGC>CAC	p.R42H	NARFL_uc002cjp.2_5'Flank|NARFL_uc002cjq.2_5'UTR|NARFL_uc002cjs.2_5'UTR|NARFL_uc010brc.1_Missense_Mutation_p.R42H|NARFL_uc010uur.1_Missense_Mutation_p.R42H	NM_022493	NP_071938	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	42					iron-sulfur cluster assembly|oxygen homeostasis|regulation of transcription, DNA-dependent|response to hypoxia		4 iron, 4 sulfur cluster binding|metal ion binding				0		Hepatocellular(780;0.0218)				ATCTTCAATGCGAATCTTGGC	0.537													23	55	---	---	---	---	PASS
SOX8	30812	broad.mit.edu	37	16	1034811	1034811	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1034811C>A	uc002ckn.2	+	3	881	c.766C>A	c.(766-768)CGC>AGC	p.R256S		NM_014587	NP_055402	P57073	SOX8_HUMAN	SRY (sex determining region Y)-box 8	256					adipose tissue development|enteric nervous system development|fat cell differentiation|in utero embryonic development|metanephric nephron tubule formation|morphogenesis of a branching epithelium|negative regulation of apoptosis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|neural crest cell migration|oligodendrocyte differentiation|osteoblast differentiation|peripheral nervous system development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of gliogenesis|positive regulation of osteoblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone levels|renal vesicle induction|retinal rod cell differentiation|Sertoli cell development|signal transduction|spermatogenesis|ureter morphogenesis	cytoplasm|nucleus				central_nervous_system(1)|skin(1)	2		Hepatocellular(780;0.00308)				GGACAGCGGGCGCCAGAACAT	0.682													6	15	---	---	---	---	PASS
GSPT1	2935	broad.mit.edu	37	16	11990652	11990652	+	Intron	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11990652G>C	uc002dbr.2	-						GSPT1_uc002dbu.2_Intron|GSPT1_uc002dbt.2_Intron|GSPT1_uc010bux.2_Intron	NM_001130007	NP_001123479	P15170	ERF3A_HUMAN	G1 to S phase transition 1 isoform 3						G1/S transition of mitotic cell cycle|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation	intracellular	GTP binding|GTPase activity|protein binding|translation release factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						ACTGAAGAAAGACATTTTAAC	0.358													4	9	---	---	---	---	PASS
GP2	2813	broad.mit.edu	37	16	20331786	20331786	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20331786C>T	uc002dgv.2	-	6	748	c.665G>A	c.(664-666)AGT>AAT	p.S222N	GP2_uc002dgw.2_Missense_Mutation_p.S219N|GP2_uc002dgx.2_Missense_Mutation_p.S75N|GP2_uc002dgy.2_Missense_Mutation_p.S72N	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	222	EGF-like.					anchored to membrane|extracellular region|plasma membrane				ovary(3)|skin(1)	4						AGGCTGCAAACTGTGGACATC	0.522													6	22	---	---	---	---	PASS
IGSF6	10261	broad.mit.edu	37	16	21655691	21655691	+	Missense_Mutation	SNP	G	C	C	rs75597368	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21655691G>C	uc002djg.1	-	3	507	c.454C>G	c.(454-456)CGG>GGG	p.R152G	uc002diq.3_Intron|METTL9_uc002dje.2_Intron|METTL9_uc002djf.2_Intron	NM_005849	NP_005840	O95976	IGSF6_HUMAN	immunoglobulin superfamily, member 6 precursor	152	Extracellular (Potential).				cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0				GBM - Glioblastoma multiforme(48;0.066)		AGGAAGCTCCGCAGTTCCTTG	0.418													12	44	---	---	---	---	PASS
RNF40	9810	broad.mit.edu	37	16	30773976	30773976	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30773976G>A	uc002dzq.2	+	2	233	c.110G>A	c.(109-111)CGT>CAT	p.R37H	C16orf93_uc002dzm.2_5'Flank|C16orf93_uc002dzn.2_5'Flank|C16orf93_uc002dzo.2_5'Flank|C16orf93_uc002dzp.2_5'Flank|RNF40_uc010caa.2_Missense_Mutation_p.R37H|RNF40_uc010cab.2_Missense_Mutation_p.R37H|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Missense_Mutation_p.R37H|RNF40_uc010vfb.1_Missense_Mutation_p.R37H	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	37					histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)			GAGCCCATTCGTCTTGGAGGC	0.597													8	38	---	---	---	---	PASS
ITGAM	3684	broad.mit.edu	37	16	31309153	31309153	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31309153G>T	uc002ebq.2	+	14	1683	c.1585G>T	c.(1585-1587)GAC>TAC	p.D529Y	ITGAM_uc002ebr.2_Missense_Mutation_p.D530Y|ITGAM_uc010cam.1_Intron|ITGAM_uc010can.2_Intron	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor	529	FG-GAP 6.|Extracellular (Potential).|Potential.				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						AGTGCTGGGGGACGTAAATGG	0.612													26	57	---	---	---	---	PASS
ABCC12	94160	broad.mit.edu	37	16	48158195	48158195	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48158195C>G	uc002efc.1	-	10	1862	c.1516G>C	c.(1516-1518)GGG>CGG	p.G506R	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA|ABCC12_uc002efe.1_Missense_Mutation_p.G506R	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	506	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				AAGATCTTCCCCTGCCAGAGA	0.537													20	46	---	---	---	---	PASS
NDRG4	65009	broad.mit.edu	37	16	58528857	58528857	+	Intron	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58528857C>T	uc002enm.2	+						NDRG4_uc002enk.2_Intron|NDRG4_uc010vif.1_Intron	NM_001130487	NP_001123959	Q9ULP0	NDRG4_HUMAN	NDRG family member 4 isoform 2						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1						CCTCTGTTTGCCTTCCCCTAG	0.577													5	10	---	---	---	---	PASS
ATP2C2	9914	broad.mit.edu	37	16	84473128	84473128	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84473128G>A	uc002fhx.2	+	13	1296	c.1207G>A	c.(1207-1209)GAG>AAG	p.E403K	ATP2C2_uc010chj.2_Missense_Mutation_p.E403K|ATP2C2_uc002fhy.2_Missense_Mutation_p.E420K|ATP2C2_uc002fhz.2_Missense_Mutation_p.E252K	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	403	Extracellular (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						GCTTCGTGCCGAGGTGAGTGC	0.493													36	72	---	---	---	---	PASS
CHD3	1107	broad.mit.edu	37	17	7814302	7814302	+	Intron	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7814302G>A	uc002gje.2	+						CHD3_uc002gjd.2_Intron|CHD3_uc002gjf.2_Intron|CHD3_uc002gjh.2_Intron|CHD3_uc002gjj.2_Intron	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)				GTCAGCTGGTGTTTTCCTACC	0.577													27	39	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11520814	11520814	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11520814G>T	uc002gne.2	+	5	1059	c.991G>T	c.(991-993)GTG>TTG	p.V331L		NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	331	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ATTTCCGGAGGTGAAGCCCCA	0.602													14	19	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11607515	11607515	+	Intron	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11607515C>A	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTCTTGCTGCCACAGGTGGCC	0.512													21	39	---	---	---	---	PASS
TAOK1	57551	broad.mit.edu	37	17	27818857	27818857	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27818857C>G	uc002hdz.1	+	10	999	c.805C>G	c.(805-807)CGA>GGA	p.R269G	TAOK1_uc010wbe.1_Missense_Mutation_p.R269G|TAOK1_uc010wbf.1_Missense_Mutation_p.R269G|TAOK1_uc002heb.1_Missense_Mutation_p.R95G	NM_020791	NP_065842	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	269	Protein kinase.				mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)			CCCTCAAGATCGACCTACATC	0.254													24	39	---	---	---	---	PASS
COPZ2	51226	broad.mit.edu	37	17	46109586	46109586	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46109586T>C	uc002imy.2	-	10	443	c.430A>G	c.(430-432)AAG>GAG	p.K144E		NM_016429	NP_057513	Q9P299	COPZ2_HUMAN	coatomer protein complex, subunit zeta 2	144					intracellular protein transport|vesicle-mediated transport	cis-Golgi network|COPI vesicle coat					0						AACCAGCGCTTCTCCACGTTC	0.597													7	25	---	---	---	---	PASS
EPX	8288	broad.mit.edu	37	17	56277147	56277147	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56277147T>C	uc002ivq.2	+	9	1615	c.1529T>C	c.(1528-1530)GTG>GCG	p.V510A		NM_000502	NP_000493	P11678	PERE_HUMAN	eosinophil peroxidase preproprotein	510					hydrogen peroxide catabolic process		heme binding|peroxidase activity|protein binding			ovary(2)	2						TGGCGGATCGTGTATGAAGGT	0.612													33	15	---	---	---	---	PASS
BZRAP1	9256	broad.mit.edu	37	17	56389036	56389036	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56389036G>A	uc002ivx.3	-	18	3848	c.2977C>T	c.(2977-2979)CCT>TCT	p.P993S	BZRAP1_uc010dcs.2_Missense_Mutation_p.P933S|BZRAP1_uc010wnt.1_Missense_Mutation_p.P993S	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	993	Fibronectin type-III 3.					mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAGATCCCAGGGGAGGGCCCA	0.622													13	32	---	---	---	---	PASS
CLTC	1213	broad.mit.edu	37	17	57754494	57754494	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57754494C>T	uc002ixq.1	+	17	3184	c.2741C>T	c.(2740-2742)CCA>CTA	p.P914L	CLTC_uc002ixp.2_Missense_Mutation_p.P914L|CLTC_uc002ixr.1_Missense_Mutation_p.P918L	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	914	Heavy chain arm.|Proximal segment.				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					AAGAGAGATCCACATCTGGCC	0.393			T	ALK|TFE3	ALCL|renal 								31	15	---	---	---	---	PASS
FTSJ3	117246	broad.mit.edu	37	17	61897535	61897535	+	Splice_Site	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61897535T>C	uc002jbz.2	-	19	2335	c.2257_splice	c.e19-1	p.M753_splice	FTSJ3_uc002jca.2_Splice_Site_p.M753_splice	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3						RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						CTTCAGCATCTGCAAAGGAAC	0.557													29	32	---	---	---	---	PASS
TEX2	55852	broad.mit.edu	37	17	62290610	62290610	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62290610G>C	uc002jec.2	-	2	1141	c.968C>G	c.(967-969)TCA>TGA	p.S323*	TEX2_uc002jed.2_Nonsense_Mutation_p.S323*|TEX2_uc002jee.2_Nonsense_Mutation_p.S323*	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2	323					signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TGAAGCACTTGAAGATAAGGC	0.453													11	46	---	---	---	---	PASS
KIF19	124602	broad.mit.edu	37	17	72349680	72349680	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72349680C>A	uc002jkm.3	+	17	2406	c.2268C>A	c.(2266-2268)GAC>GAA	p.D756E		NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	756					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						CTTCCCCTGACAGCAGTGAGA	0.597													20	13	---	---	---	---	PASS
KIF19	124602	broad.mit.edu	37	17	72349681	72349681	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72349681A>G	uc002jkm.3	+	17	2407	c.2269A>G	c.(2269-2271)AGC>GGC	p.S757G		NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	757					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						TTCCCCTGACAGCAGTGAGAA	0.597													21	12	---	---	---	---	PASS
SLC25A19	60386	broad.mit.edu	37	17	73279678	73279678	+	Intron	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73279678C>G	uc002jns.3	-						SLC25A19_uc010dge.2_Intron|SLC25A19_uc002jnv.3_Intron|SLC25A19_uc002jnu.3_Intron|SLC25A19_uc002jnw.3_Intron|SLC25A19_uc002jnt.3_Intron	NM_021734	NP_068380	Q9HC21	TPC_HUMAN	solute carrier family 25, member 19							integral to membrane|mitochondrial inner membrane	binding|deoxynucleotide transmembrane transporter activity			ovary(1)	1	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			ACAAGAACTGCAAGAGTAAGT	0.552													10	9	---	---	---	---	PASS
CCDC40	55036	broad.mit.edu	37	17	78058646	78058646	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78058646G>A	uc010dht.2	+	13	2121	c.2094G>A	c.(2092-2094)CTG>CTA	p.L698L	CCDC40_uc002jxm.3_Silent_p.L481L|CCDC40_uc002jxn.3_Silent_p.L94L	NM_017950	NP_060420	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	698	Potential.				axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm				ovary(3)	3	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TGGTGGAGCTGGACCAGGACG	0.562													10	35	---	---	---	---	PASS
SIRT7	51547	broad.mit.edu	37	17	79872183	79872183	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79872183C>A	uc002kcj.1	-	7	836	c.803G>T	c.(802-804)GGG>GTG	p.G268V	PCYT2_uc002kcf.1_5'Flank|PCYT2_uc002kcg.1_5'Flank|PCYT2_uc002kch.1_5'Flank|PCYT2_uc002kci.1_5'Flank|PCYT2_uc010dii.1_5'Flank|PCYT2_uc010wvc.1_5'Flank|SIRT7_uc002kck.1_Missense_Mutation_p.G119V|SIRT7_uc002kcl.1_Missense_Mutation_p.G186V	NM_016538	NP_057622	Q9NRC8	SIRT7_HUMAN	sirtuin 7	268	Deacetylase sirtuin-type.				chromatin silencing|positive regulation of transcription on exit from mitosis|protein deacetylation|rRNA transcription	cytoplasm|nucleolus organizer region	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ binding|protein binding|zinc ion binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CAGGCTGGACCCTAGACACAG	0.617													23	25	---	---	---	---	PASS
THOC1	9984	broad.mit.edu	37	18	264100	264100	+	Intron	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:264100C>A	uc002kkj.3	-						THOC1_uc002kkk.3_Intron|THOC1_uc002kkl.2_Intron	NM_005131	NP_005122	Q96FV9	THOC1_HUMAN	THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				TATCTACCAACAGAGGAGAAA	0.328													10	10	---	---	---	---	PASS
CTAGE1	64693	broad.mit.edu	37	18	19996144	19996144	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19996144C>A	uc002ktv.1	-	1	1735	c.1631G>T	c.(1630-1632)GGA>GTA	p.G544V		NM_172241	NP_758441	Q96RT6	CTGE2_HUMAN	cutaneous T-cell lymphoma-associated antigen 1	544						integral to membrane				ovary(1)	1	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					GCTTGATTCTCCTCTTTCTTT	0.547													16	59	---	---	---	---	PASS
DSC1	1823	broad.mit.edu	37	18	28719713	28719713	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28719713G>T	uc002kwn.2	-	11	1923	c.1661C>A	c.(1660-1662)GCA>GAA	p.A554E	DSC1_uc002kwm.2_Missense_Mutation_p.A554E	NM_024421	NP_077739	Q08554	DSC1_HUMAN	desmocollin 1 isoform Dsc1a preproprotein	554	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			GCACTCACCTGCATCCACTGC	0.313													5	14	---	---	---	---	PASS
MEP1B	4225	broad.mit.edu	37	18	29793520	29793520	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29793520C>A	uc002kxj.3	+	11	1624	c.1577C>A	c.(1576-1578)ACC>AAC	p.T526N		NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor	526	Extracellular (Potential).|MATH.				digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2						TTTATGACCACCGGTTCGTAA	0.418													15	60	---	---	---	---	PASS
FAM59A	64762	broad.mit.edu	37	18	29867260	29867260	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29867260G>T	uc002kxl.2	-	4	1356	c.1300C>A	c.(1300-1302)CTT>ATT	p.L434I	FAM59A_uc002kxk.1_Missense_Mutation_p.L434I	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	434										ovary(1)|skin(1)	2						TCTGGGAAAAGGTAGTCGCTC	0.562													31	75	---	---	---	---	PASS
C18orf34	374864	broad.mit.edu	37	18	30873191	30873191	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30873191C>A	uc002kxn.2	-	11	1250	c.1108G>T	c.(1108-1110)GAG>TAG	p.E370*	C18orf34_uc010xbr.1_Nonsense_Mutation_p.E370*|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Nonsense_Mutation_p.E370*|C18orf34_uc002kxp.2_Nonsense_Mutation_p.E370*	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	370	Potential.									ovary(1)	1						GTCACTTCCTCTTCCTTCTCC	0.289													5	28	---	---	---	---	PASS
ELP2	55250	broad.mit.edu	37	18	33710009	33710009	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33710009G>T	uc002kzk.1	+	1	123	c.113G>T	c.(112-114)TGC>TTC	p.C38F	SLC39A6_uc010dmy.2_5'Flank|SLC39A6_uc002kzj.2_5'Flank|ELP2_uc010xcg.1_Missense_Mutation_p.C38F|ELP2_uc002kzl.1_RNA|ELP2_uc002kzm.1_Missense_Mutation_p.C38F|ELP2_uc010xch.1_Missense_Mutation_p.C38F|ELP2_uc002kzn.1_Missense_Mutation_p.C38F|ELP2_uc002kzo.1_Missense_Mutation_p.C38F	NM_018255	NP_060725	Q6IA86	ELP2_HUMAN	elongator protein 2	38	WD 1.				regulation of transcription from RNA polymerase II promoter	Golgi apparatus|transcription elongation factor complex				breast(2)|ovary(1)|skin(1)	4						GGCACGTCCTGCTCCGTGGTG	0.622													11	29	---	---	---	---	PASS
DCC	1630	broad.mit.edu	37	18	50592439	50592439	+	Silent	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50592439T>A	uc002lfe.1	+	7	1751	c.1164T>A	c.(1162-1164)CTT>CTA	p.L388L	DCC_uc010xdr.1_Silent_p.L236L|DCC_uc010dpf.1_Silent_p.L43L	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	388	Extracellular (Potential).|Ig-like C2-type 4.				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TACGGATACTTGGGGTGGTGA	0.433													26	97	---	---	---	---	PASS
DSEL	92126	broad.mit.edu	37	18	65181699	65181699	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65181699A>T	uc002lke.1	-	2	1401	c.177T>A	c.(175-177)GAT>GAA	p.D59E		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	49						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)				TGGGTCTGAAATCTTGCACTT	0.378													14	47	---	---	---	---	PASS
LPHN1	22859	broad.mit.edu	37	19	14273977	14273977	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14273977C>A	uc010xnn.1	-	6	947	c.651G>T	c.(649-651)GTG>GTT	p.V217V	LPHN1_uc010xno.1_Silent_p.V212V|uc002myf.2_Intron	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	217	Olfactomedin-like.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5						CATCGTAGACCACAAAGCCTG	0.602													4	21	---	---	---	---	PASS
ZNF43	7594	broad.mit.edu	37	19	21991722	21991722	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21991722T>C	uc002nqj.2	-	4	1247	c.1117A>G	c.(1117-1119)ACA>GCA	p.T373A	ZNF43_uc010ecv.2_Missense_Mutation_p.T367A|ZNF43_uc002nql.2_Missense_Mutation_p.T367A|ZNF43_uc002nqm.2_Missense_Mutation_p.T367A|ZNF43_uc002nqk.2_Missense_Mutation_p.T303A	NM_003423	NP_003414	P17038	ZNF43_HUMAN	zinc finger protein 43	373	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		CCACATTCTGTACATTTATAG	0.373													17	32	---	---	---	---	PASS
CCNE1	898	broad.mit.edu	37	19	30313189	30313189	+	Missense_Mutation	SNP	C	A	A	rs139792204	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30313189C>A	uc002nsn.2	+	10	1066	c.883C>A	c.(883-885)CCT>ACT	p.P295T	CCNE1_uc002nso.2_Missense_Mutation_p.P280T|CCNE1_uc002nsp.2_Missense_Mutation_p.P42T	NM_001238	NP_001229	P24864	CCNE1_HUMAN	cyclin E1 isoform 1	295					androgen receptor signaling pathway|cell division|positive regulation of transcription, DNA-dependent|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm	androgen receptor binding|protein kinase binding|transcription coactivator activity			lung(2)	2	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			CCTTGAATTTCCTTATGGTAT	0.453													28	66	---	---	---	---	PASS
GAPDHS	26330	broad.mit.edu	37	19	36034322	36034322	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36034322C>A	uc002oaf.1	+	8	938	c.822C>A	c.(820-822)GCC>GCA	p.A274A	uc010eec.1_RNA|uc002oag.2_Intron|TMEM147_uc002oai.1_5'Flank|TMEM147_uc002oaj.1_5'Flank|TMEM147_uc002oak.1_5'Flank	NM_014364	NP_055179	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase,	274					gluconeogenesis|glycolysis|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		NADH(DB00157)	GGCGGGGTGCCCACCAGAACA	0.587													15	40	---	---	---	---	PASS
ZNF527	84503	broad.mit.edu	37	19	37880462	37880462	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37880462G>A	uc010efk.1	+	5	1622	c.1511G>A	c.(1510-1512)GGG>GAG	p.G504E	ZNF527_uc002ogf.3_Missense_Mutation_p.G472E|ZNF527_uc010xtq.1_RNA	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527	504	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGTAAATGTGGGAAAGCCTTC	0.393													21	65	---	---	---	---	PASS
ZNF781	163115	broad.mit.edu	37	19	38160382	38160382	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38160382A>G	uc002ogy.2	-	4	1410	c.668T>C	c.(667-669)ATA>ACA	p.I223T	ZNF781_uc002ogz.2_Missense_Mutation_p.I218T	NM_152605	NP_689818	Q8N8C0	ZN781_HUMAN	zinc finger protein 781	223					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCTCACCAGTATGAATTCTTT	0.358													4	44	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38572647	38572647	+	Missense_Mutation	SNP	G	C	C	rs138476311	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38572647G>C	uc002ohk.2	+	3	951	c.442G>C	c.(442-444)GAC>CAC	p.D148H		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	148					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AAGGTCCAAAGACGTGGAGTT	0.657													18	59	---	---	---	---	PASS
MAP4K1	11184	broad.mit.edu	37	19	39078377	39078377	+	3'UTR	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39078377C>A	uc002oix.1	-	32					MAP4K1_uc002oiw.1_3'UTR|MAP4K1_uc002oiy.1_3'UTR	NM_007181	NP_009112	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCCTGACACCCCCCTAGGGAC	0.537													6	27	---	---	---	---	PASS
IL28A	282616	broad.mit.edu	37	19	39760578	39760578	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39760578C>T	uc002oku.1	+	6	580	c.528C>T	c.(526-528)GCC>GCT	p.A176A		NM_172138	NP_742150	Q8IZJ0	IL28A_HUMAN	interleukin 28A precursor	176					response to virus	extracellular space	cytokine activity			ovary(1)|skin(1)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;5.39e-26)|all cancers(26;4.1e-23)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GCCTCGAGGCCTCTGTCACCT	0.627													7	10	---	---	---	---	PASS
IRGQ	126298	broad.mit.edu	37	19	44096971	44096971	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44096971C>T	uc002oww.2	-	2	1197	c.1079G>A	c.(1078-1080)GGG>GAG	p.G360E	IRGQ_uc010eiv.2_Missense_Mutation_p.G360E	NM_001007561	NP_001007562	Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	360	Poly-Gly.						protein binding			ovary(1)|pancreas(1)	2		Prostate(69;0.0199)				CTCCAATCCCCCTCCACCTGC	0.597													36	110	---	---	---	---	PASS
TOMM40	10452	broad.mit.edu	37	19	45397079	45397079	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45397079C>G	uc002ozx.3	+	5	579	c.478C>G	c.(478-480)CTC>GTC	p.L160V	TOMM40_uc002ozy.3_Missense_Mutation_p.L160V|TOMM40_uc002paa.3_Missense_Mutation_p.L160V|TOMM40_uc002ozz.2_Missense_Mutation_p.L160V	NM_006114	NP_006105	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40	160					protein targeting to mitochondrion	integral to membrane of membrane fraction|integral to mitochondrial outer membrane|mitochondrial outer membrane translocase complex|pore complex	porin activity|protein transmembrane transporter activity|voltage-gated anion channel activity				0	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		CAGTGGCAGTCTCAACGCTCA	0.612													7	25	---	---	---	---	PASS
PPP1R13L	10848	broad.mit.edu	37	19	45888902	45888902	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45888902G>A	uc002pbn.2	-	11	2243	c.2166C>T	c.(2164-2166)ACC>ACT	p.T722T	PPP1R13L_uc002pbm.2_Silent_p.T301T|PPP1R13L_uc002pbo.2_Silent_p.T722T	NM_006663	NP_006654	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13	722	ANK 2.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	transcription corepressor activity|transcription factor binding			skin(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		CGCTGAGCGTGGTGGCGAAGA	0.667													4	16	---	---	---	---	PASS
CARD8	22900	broad.mit.edu	37	19	48734082	48734082	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48734082C>G	uc002pie.3	-	5	722	c.409G>C	c.(409-411)GAG>CAG	p.E137Q	CARD8_uc002pii.3_Missense_Mutation_p.E242Q|CARD8_uc010xzi.1_Missense_Mutation_p.E137Q|CARD8_uc010els.2_Missense_Mutation_p.E175Q|CARD8_uc010xzj.1_Missense_Mutation_p.E242Q|CARD8_uc010xzk.1_Missense_Mutation_p.E161Q|CARD8_uc002pif.3_Missense_Mutation_p.E137Q|CARD8_uc002pig.3_5'UTR|CARD8_uc002pih.3_Missense_Mutation_p.E192Q|CARD8_uc010xzl.1_Missense_Mutation_p.E192Q|CARD8_uc010xzm.1_Missense_Mutation_p.E242Q	NM_014959	NP_055774	Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	137					negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		ACAGCCTCCTCTGGCTCTGCA	0.632													14	44	---	---	---	---	PASS
IZUMO1	284359	broad.mit.edu	37	19	49248554	49248554	+	Intron	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49248554G>A	uc002pkj.2	-						IZUMO1_uc010eme.2_Intron|IZUMO1_uc010emf.2_Intron	NM_182575	NP_872381	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1 precursor						fusion of sperm to egg plasma membrane	integral to membrane				ovary(1)	1		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		ATCTGTCAGAGGAGATATAAC	0.483													16	32	---	---	---	---	PASS
SIGLEC11	114132	broad.mit.edu	37	19	50462101	50462101	+	Missense_Mutation	SNP	G	T	T	rs145434757	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50462101G>T	uc010ybh.1	-	7	1253	c.1162C>A	c.(1162-1164)CGC>AGC	p.R388S	SIGLEC11_uc010ybi.1_Missense_Mutation_p.R388S	NM_052884	NP_443116	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11 isoform 1	388	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|central_nervous_system(2)|pancreas(1)	6		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		CAGACCAGGCGCAGGCTTTGG	0.677													12	18	---	---	---	---	PASS
ZNF473	25888	broad.mit.edu	37	19	50549003	50549003	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50549003G>C	uc002prn.2	+	5	1540	c.1303G>C	c.(1303-1305)GAG>CAG	p.E435Q	ZNF473_uc002prm.2_Missense_Mutation_p.E435Q|ZNF473_uc010ybo.1_Missense_Mutation_p.E423Q	NM_001006656	NP_001006657	Q8WTR7	ZN473_HUMAN	zinc finger protein 473	435	C2H2-type 7.|Interaction with SLBP/pre-mRNA complex.				histone mRNA 3'-end processing|regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription	Cajal body	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		CAAATGCAGTGAGTGTGGGAA	0.483													37	50	---	---	---	---	PASS
ZNF473	25888	broad.mit.edu	37	19	50549375	50549375	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50549375G>C	uc002prn.2	+	5	1912	c.1675G>C	c.(1675-1677)GAG>CAG	p.E559Q	ZNF473_uc002prm.2_Missense_Mutation_p.E559Q|ZNF473_uc010ybo.1_Missense_Mutation_p.E547Q	NM_001006656	NP_001006657	Q8WTR7	ZN473_HUMAN	zinc finger protein 473	559					histone mRNA 3'-end processing|regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription	Cajal body	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		AGAACAGAAAGAGAAGTGCTT	0.458													27	26	---	---	---	---	PASS
SHANK1	50944	broad.mit.edu	37	19	51200905	51200905	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51200905C>T	uc002psx.1	-	13	1897	c.1878G>A	c.(1876-1878)AAG>AAA	p.K626K		NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	626					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GTCTCTTTGCCTTGTCACTGC	0.547													22	96	---	---	---	---	PASS
CD33	945	broad.mit.edu	37	19	51729094	51729094	+	Missense_Mutation	SNP	A	T	T	rs149059669		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51729094A>T	uc002pwa.2	+	3	494	c.454A>T	c.(454-456)ACT>TCT	p.T152S	CD33_uc010eos.1_Missense_Mutation_p.T152S|CD33_uc010eot.1_Missense_Mutation_p.T25S|CD33_uc010eou.1_RNA	NM_001772	NP_001763	P20138	CD33_HUMAN	CD33 antigen isoform 1 precursor	152	Extracellular (Potential).|Ig-like C2-type.				cell adhesion|cell-cell signaling|negative regulation of cell proliferation	external side of plasma membrane|integral to plasma membrane	receptor activity|sugar binding				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	CATCCCTGGCACTCTAGAACC	0.587													61	69	---	---	---	---	PASS
C19orf75	284369	broad.mit.edu	37	19	51769043	51769043	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51769043T>C	uc002pwb.1	+	4	698	c.317T>C	c.(316-318)TTG>TCG	p.L106S	C19orf75_uc010eov.1_RNA|C19orf75_uc010ycw.1_Missense_Mutation_p.L12S	NM_173635	NP_775906	Q8N7X8	CS075_HUMAN	hypothetical protein LOC284369	106						integral to membrane				ovary(1)|pancreas(1)	2						AAGAGTTCTTTGGCTGCCCAG	0.537													46	215	---	---	---	---	PASS
VN1R4	317703	broad.mit.edu	37	19	53770038	53770038	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53770038C>A	uc010ydu.1	-	1	881	c.881G>T	c.(880-882)AGG>ATG	p.R294M		NM_173857	NP_776256	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	294	Cytoplasmic (Potential).				response to pheromone	actin cytoskeleton|cytoplasm|integral to membrane|plasma membrane	pheromone receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.00294)		AAAACAAAACCTGTATACACT	0.393										HNSCC(26;0.072)			9	86	---	---	---	---	PASS
LILRB2	10288	broad.mit.edu	37	19	54783637	54783637	+	Intron	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54783637T>C	uc002qfb.2	-						LILRA6_uc002qew.1_Intron|LILRB2_uc010eri.2_Intron|LILRB2_uc010erj.2_Intron|LILRB2_uc002qfc.2_Intron|LILRB2_uc010yet.1_Intron|LILRB2_uc010yeu.1_Intron	NM_005874	NP_005865	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|cell-cell signaling|cellular defense response|immune response|regulation of immune response	integral to plasma membrane|membrane fraction	receptor activity			skin(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCCCTGAGTGTCCTCTCACCT	0.627													49	67	---	---	---	---	PASS
KIR3DX1	90011	broad.mit.edu	37	19	55046802	55046802	+	5'Flank	SNP	C	A	A	rs143059017	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55046802C>A	uc010erm.2	+						KIR3DX1_uc010yfa.1_Intron|KIR3DX1_uc010yfb.1_Intron|KIR3DX1_uc010yfc.1_Intron|KIR3DX1_uc010yfd.1_Intron					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		TCTCTGCTCTCAGGCTTGTTC	0.592													17	80	---	---	---	---	PASS
KIR2DS4	3809	broad.mit.edu	37	19	55349311	55349311	+	Silent	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55349311T>C	uc002qhm.1	+	3	397	c.351T>C	c.(349-351)CCT>CCC	p.P117P	KIR2DS4_uc010yfj.1_Silent_p.P110P|KIR2DS4_uc010yfk.1_RNA|KIR3DL1_uc002qhl.3_Intron|KIR2DS4_uc010esg.1_Silent_p.P117P|KIR2DS4_uc002qhn.1_Silent_p.P64P	NM_012314	NP_036446	P43632	KI2S4_HUMAN	killer cell immunoglobulin-like receptor, two	117	Extracellular (Potential).					integral to plasma membrane	receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)		CCAGTGACCCTCTGGACATGG	0.507													11	379	---	---	---	---	PASS
EPS8L1	54869	broad.mit.edu	37	19	55594735	55594735	+	Intron	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55594735C>T	uc002qis.3	+						EPS8L1_uc010ess.1_Intron|EPS8L1_uc010est.1_Intron|EPS8L1_uc010yfr.1_Intron|EPS8L1_uc010esu.1_Intron|EPS8L1_uc002qiu.2_Intron|EPS8L1_uc002qiv.2_Intron|EPS8L1_uc002qiw.2_Intron	NM_133180	NP_573441	Q8TE68	ES8L1_HUMAN	epidermal growth factor receptor pathway							cytoplasm					0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TGGCCCTGTCCCTGGCCGCAG	0.607													13	20	---	---	---	---	PASS
TMEM150B	284417	broad.mit.edu	37	19	55832413	55832413	+	Splice_Site	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55832413C>G	uc010esw.1	-	3	166	c.-7_splice	c.e3-1		TMEM150B_uc010yfu.1_5'UTR|TMEM150B_uc010yfv.1_RNA|TMEM150B_uc010yfw.1_Splice_Site|TMEM150B_uc002qki.2_5'UTR	NM_001085488	NP_001078957	A6NC51	T150B_HUMAN	transmembrane protein 150B precursor							integral to membrane					0						ATGCCGGGCTCTGCAGGTGAA	0.597													14	16	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56369842	56369842	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56369842G>T	uc002qmd.3	+	3	1505	c.1083G>T	c.(1081-1083)CTG>CTT	p.L361L	NLRP4_uc002qmf.2_Silent_p.L286L|NLRP4_uc010etf.2_Silent_p.L192L	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	361	NACHT.						ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GAAAAGACCTGGCCCTGACCT	0.532													27	30	---	---	---	---	PASS
ZNF211	10520	broad.mit.edu	37	19	58152141	58152141	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58152141A>C	uc002qpq.2	+	3	467	c.287A>C	c.(286-288)CAG>CCG	p.Q96P	ZNF211_uc010yhb.1_Missense_Mutation_p.Q100P|ZNF211_uc002qpp.2_Missense_Mutation_p.Q109P|ZNF211_uc002qpr.2_Missense_Mutation_p.Q160P|ZNF211_uc002qps.2_Missense_Mutation_p.Q161P|ZNF211_uc002qpt.2_Missense_Mutation_p.Q108P|ZNF211_uc010yhc.1_Missense_Mutation_p.Q108P|ZNF211_uc010yhd.1_Missense_Mutation_p.Q35P|ZNF211_uc010yhe.1_Missense_Mutation_p.Q87P	NM_198855	NP_942152	Q13398	ZN211_HUMAN	zinc finger protein 211 isoform 2	96	KRAB.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGAGTGCCACAGTTCAGGACT	0.433													9	38	---	---	---	---	PASS
ZNF211	10520	broad.mit.edu	37	19	58153536	58153536	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58153536G>T	uc002qpq.2	+	3	1862	c.1682G>T	c.(1681-1683)GGA>GTA	p.G561V	ZNF211_uc010yhb.1_Missense_Mutation_p.G565V|ZNF211_uc002qpp.2_Missense_Mutation_p.G574V|ZNF211_uc002qpr.2_Missense_Mutation_p.G625V|ZNF211_uc002qps.2_Missense_Mutation_p.G626V|ZNF211_uc002qpt.2_Missense_Mutation_p.G573V|ZNF211_uc010yhc.1_Missense_Mutation_p.G573V|ZNF211_uc010yhd.1_Missense_Mutation_p.G500V|ZNF211_uc010yhe.1_Missense_Mutation_p.G552V	NM_198855	NP_942152	Q13398	ZN211_HUMAN	zinc finger protein 211 isoform 2	561						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTTCACATTGGAGAAAAGCCT	0.433													33	120	---	---	---	---	PASS
ZNF587	84914	broad.mit.edu	37	19	58262285	58262285	+	Intron	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58262285G>T	uc002qqb.2	+						ZNF776_uc002qpx.2_Intron|ZNF776_uc002qqa.2_Intron	NM_032828	NP_116217	Q96SQ5	ZN587_HUMAN	zinc finger protein 587						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		TCTAGGTAAGGCACTCACACT	0.483													9	38	---	---	---	---	PASS
ZNF135	7694	broad.mit.edu	37	19	58579130	58579130	+	Silent	SNP	C	T	T	rs141591921		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58579130C>T	uc010yhq.1	+	5	1410	c.1314C>T	c.(1312-1314)ACC>ACT	p.T438T	ZNF135_uc002qre.2_Silent_p.T426T|ZNF135_uc002qrd.1_Intron|ZNF135_uc002qrf.2_Silent_p.T384T|ZNF135_uc002qrg.2_Silent_p.T396T|ZNF135_uc010yhr.1_Silent_p.T247T	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135 isoform 2	438					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		CACTCCTGACCGAGCATCGGA	0.547													24	59	---	---	---	---	PASS
ANGPT4	51378	broad.mit.edu	37	20	896599	896599	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:896599C>G	uc002wei.2	-	1	362	c.259G>C	c.(259-261)GTG>CTG	p.V87L	ANGPT4_uc010zpn.1_Missense_Mutation_p.V81L	NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4 precursor	87	Potential.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2						AGCTGTTTCACCTGCTGGGTG	0.637													15	59	---	---	---	---	PASS
SIRPB1	10326	broad.mit.edu	37	20	1552435	1552435	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1552435C>A	uc010gai.2	-	3	781	c.682G>T	c.(682-684)GAG>TAG	p.E228*	SIRPB1_uc002wfk.3_Intron	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1	228	Ig-like C1-type 1.|Extracellular (Potential).				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1						TGGGCTATCTCGCAGATGACT	0.607													20	59	---	---	---	---	PASS
ADAM33	80332	broad.mit.edu	37	20	3652789	3652789	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3652789C>G	uc002wit.2	-	14	1676	c.1589G>C	c.(1588-1590)TGG>TCG	p.W530S	ADAM33_uc002wiq.1_5'Flank|ADAM33_uc002wir.1_Missense_Mutation_p.W530S|ADAM33_uc002wis.2_Missense_Mutation_p.W52S|ADAM33_uc002wiu.2_Missense_Mutation_p.W530S|uc002wiv.1_5'Flank|ADAM33_uc002wiw.1_Intron|ADAM33_uc010gba.1_Intron|ADAM33_uc010gbb.1_Intron	NM_025220	NP_079496	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33 isoform alpha	530	Extracellular (Potential).|Cys-rich.				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|ovary(1)|skin(1)	4						ACCAGGCCCCCAGAGCTGCTG	0.642													9	20	---	---	---	---	PASS
CHGB	1114	broad.mit.edu	37	20	5904410	5904410	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5904410C>A	uc002wmg.2	+	4	1926	c.1620C>A	c.(1618-1620)GAC>GAA	p.D540E	CHGB_uc010zqz.1_Missense_Mutation_p.D223E	NM_001819	NP_001810	P05060	SCG1_HUMAN	chromogranin B precursor	540						extracellular region	hormone activity			breast(3)|skin(2)|ovary(1)	6						AAAGAAGAGACAACATGAATG	0.448													18	58	---	---	---	---	PASS
PLCB1	23236	broad.mit.edu	37	20	8862385	8862385	+	Silent	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8862385T>C	uc002wnb.2	+	32	3543	c.3540T>C	c.(3538-3540)GGT>GGC	p.G1180G	PLCB1_uc002wna.2_3'UTR	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	1180					activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						GCAATCACGGTTCTGCCCCTC	0.483													53	186	---	---	---	---	PASS
PLCB4	5332	broad.mit.edu	37	20	9368183	9368183	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9368183T>A	uc002wnf.2	+	14	1274	c.1138T>A	c.(1138-1140)TGT>AGT	p.C380S	PLCB4_uc010gbw.1_Missense_Mutation_p.C380S|PLCB4_uc010gbx.2_Missense_Mutation_p.C380S|PLCB4_uc002wne.2_Missense_Mutation_p.C380S|PLCB4_uc002wnh.2_Missense_Mutation_p.C227S	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	380	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						AAAAGCAATGTGTACAGATAT	0.343													16	32	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20486105	20486105	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20486105C>A	uc002wrz.2	-	34	5145	c.5002G>T	c.(5002-5004)GAA>TAA	p.E1668*	RALGAPA2_uc010gcx.2_Nonsense_Mutation_p.E1372*|RALGAPA2_uc010zsg.1_Nonsense_Mutation_p.E1116*|RALGAPA2_uc002wsa.1_Nonsense_Mutation_p.E440*	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1668	Rap-GAP.				activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						CTTCCTCTTTCATTAGAGAGG	0.373													5	12	---	---	---	---	PASS
DNMT3B	1789	broad.mit.edu	37	20	31380550	31380550	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31380550G>A	uc002wyc.2	+	9	1361	c.1040G>A	c.(1039-1041)GGC>GAC	p.G347D	DNMT3B_uc010ztx.1_RNA|DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Missense_Mutation_p.G347D|DNMT3B_uc002wye.2_Missense_Mutation_p.G347D|DNMT3B_uc010gee.2_RNA|DNMT3B_uc010gef.2_RNA|DNMT3B_uc010ztz.1_Missense_Mutation_p.G305D|DNMT3B_uc010zua.1_Missense_Mutation_p.G271D|DNMT3B_uc002wyf.2_Missense_Mutation_p.G359D|DNMT3B_uc002wyg.2_Missense_Mutation_p.G46D	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform	347					negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5						GGGATCGAGGGCCTCAAACCC	0.632													20	32	---	---	---	---	PASS
SLC32A1	140679	broad.mit.edu	37	20	37356487	37356487	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37356487G>T	uc002xjc.2	+	2	1046	c.783G>T	c.(781-783)AAG>AAT	p.K261N		NM_080552	NP_542119	Q9H598	VIAAT_HUMAN	solute carrier family 32, member 1	261	Helical; (Potential).			K -> R (in Ref. 4; AAH36458).	neurotransmitter secretion	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|integral to membrane|plasma membrane|synaptic vesicle membrane	vesicular hydrogen:amino acid antiporter activity				0		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	AGAACCTCAAGGCCGTGTCCA	0.597													9	19	---	---	---	---	PASS
DHX35	60625	broad.mit.edu	37	20	37657096	37657096	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37657096G>A	uc002xjh.2	+	19	1848	c.1837G>A	c.(1837-1839)GGC>AGC	p.G613S	DHX35_uc010zwa.1_Missense_Mutation_p.G458S|DHX35_uc010zwb.1_Missense_Mutation_p.G458S|DHX35_uc010zwc.1_Missense_Mutation_p.G582S	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	613						catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				CATTGTCTCCGGCTTCTTCGC	0.493													32	62	---	---	---	---	PASS
SEMG1	6406	broad.mit.edu	37	20	43836175	43836175	+	Silent	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43836175C>T	uc002xni.2	+	2	294	c.237C>T	c.(235-237)TCC>TCT	p.S79S	SEMG1_uc002xnj.2_Silent_p.S79S|SEMG2_uc010ggz.2_Intron|SEMG1_uc002xnh.2_Silent_p.S79S	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I preproprotein	79					insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(2)	2		Myeloproliferative disorder(115;0.0122)				ATGACCAGTCCCGAAAAAGTC	0.383													18	79	---	---	---	---	PASS
ZNF217	7764	broad.mit.edu	37	20	52193465	52193465	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52193465T>A	uc002xwq.3	-	3	2109	c.1838A>T	c.(1837-1839)AAA>ATA	p.K613I	ZNF217_uc010gij.1_Missense_Mutation_p.K605I	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	613					negative regulation of transcription, DNA-dependent	histone deacetylase complex	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1)	6	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TTTATTCACTTTATCAGCACT	0.438													23	36	---	---	---	---	PASS
PHACTR3	116154	broad.mit.edu	37	20	58318296	58318296	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58318296A>G	uc002yau.2	+	2	720	c.253A>G	c.(253-255)AAC>GAC	p.N85D	PHACTR3_uc002yat.2_Missense_Mutation_p.N82D|PHACTR3_uc010zzw.1_Missense_Mutation_p.N44D|PHACTR3_uc002yav.2_Missense_Mutation_p.N44D|PHACTR3_uc002yaw.2_Missense_Mutation_p.N44D|PHACTR3_uc002yax.2_Missense_Mutation_p.N44D	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	85						nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			GAAAAAGAAAAACGAAAAACT	0.567													17	39	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	21	10862644	10862644	+	IGR	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10862644T>A								None (None upstream) : TPTE (44099 downstream)																							TGGAGGATCCTGTTTTTGGTG	0.502													26	279	---	---	---	---	PASS
KRTAP13-2	337959	broad.mit.edu	37	21	31744283	31744283	+	Silent	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31744283G>A	uc002ynz.3	-	1	275	c.249C>T	c.(247-249)CCC>CCT	p.P83P		NM_181621	NP_853652	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	83	4.|5 X 10 AA approximate repeats.					intermediate filament					0						AGGAGGTTCTGGGGCGGTAGC	0.607													16	33	---	---	---	---	PASS
KRTAP13-3	337960	broad.mit.edu	37	21	31797811	31797811	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31797811C>G	uc002yob.1	-	1	420	c.420G>C	c.(418-420)CAG>CAC	p.Q140H		NM_181622	NP_853653	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	140						intermediate filament				ovary(1)|lung(1)	2						ATCTATAACTCTGGGAAGGGG	0.468													8	22	---	---	---	---	PASS
PWP2	5822	broad.mit.edu	37	21	45548185	45548185	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45548185T>C	uc002zeb.2	+	19	2507	c.2417T>C	c.(2416-2418)TTA>TCA	p.L806S		NM_005049	NP_005040	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog	806						cytoplasm|nucleolus	signal transducer activity			pancreas(1)	1				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		CTGGAGTTTTTAGCTTCCTCC	0.478													18	44	---	---	---	---	PASS
TRPM2	7226	broad.mit.edu	37	21	45815337	45815337	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45815337C>G	uc002zet.1	+	13	2048	c.1835C>G	c.(1834-1836)TCA>TGA	p.S612*	TRPM2_uc002zeu.1_Nonsense_Mutation_p.S612*|TRPM2_uc002zew.1_Nonsense_Mutation_p.S612*|TRPM2_uc010gpt.1_Nonsense_Mutation_p.S612*|TRPM2_uc002zex.1_Nonsense_Mutation_p.S398*|TRPM2_uc002zey.1_Nonsense_Mutation_p.S125*	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	612	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						AAGCGTTCCTCAGGCCATGTG	0.502													26	90	---	---	---	---	PASS
ITGB2	3689	broad.mit.edu	37	21	46310005	46310005	+	Silent	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46310005C>A	uc002zgd.2	-	11	1589	c.1545G>T	c.(1543-1545)GGG>GGT	p.G515G	ITGB2_uc002zge.2_Silent_p.G515G|ITGB2_uc002zgf.3_Silent_p.G515G|ITGB2_uc011afl.1_Silent_p.G437G|ITGB2_uc010gpw.2_Silent_p.G458G|ITGB2_uc002zgg.2_Silent_p.G515G	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	515	II.|Extracellular (Potential).|Cysteine-rich tandem repeats.				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)	ACAGGCACTGCCCGCAGACAC	0.617													7	25	---	---	---	---	PASS
CSF2RB	1439	broad.mit.edu	37	22	37322057	37322057	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37322057C>T	uc003aqa.3	+	4	446	c.229C>T	c.(229-231)CTC>TTC	p.L77F	CSF2RB_uc003aqc.3_Missense_Mutation_p.L77F	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	77	Extracellular (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)	GTCCTGTGACCTCAGTGATGA	0.502													8	10	---	---	---	---	PASS
POLR3H	171568	broad.mit.edu	37	22	41926859	41926859	+	Silent	SNP	G	A	A	rs140901049	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41926859G>A	uc003baf.2	-	6	453	c.393C>T	c.(391-393)TAC>TAT	p.Y131Y	POLR3H_uc003bae.2_RNA|POLR3H_uc003bag.2_Silent_p.Y131Y|POLR3H_uc003bai.2_Silent_p.Y102Y	NM_138338	NP_612211	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	131					innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity			skin(1)	1						CCTCCGTCTCGTACTCCCACA	0.642													15	24	---	---	---	---	PASS
FRMPD4	9758	broad.mit.edu	37	X	12735105	12735105	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12735105G>T	uc004cuz.1	+	15	3033	c.2527G>T	c.(2527-2529)GAT>TAT	p.D843Y	FRMPD4_uc011mij.1_Missense_Mutation_p.D835Y	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	843					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						CCTGCAAAATGATGAGATCCC	0.577													30	25	---	---	---	---	PASS
MED14	9282	broad.mit.edu	37	X	40539210	40539210	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40539210C>T	uc004dex.3	-	21	2926	c.2786G>A	c.(2785-2787)CGG>CAG	p.R929Q		NM_004229	NP_004220	O60244	MED14_HUMAN	mediator complex subunit 14	929					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4						ACCTCGACTCCGGCAGTATAT	0.463													6	24	---	---	---	---	PASS
DGKK	139189	broad.mit.edu	37	X	50136227	50136227	+	Silent	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50136227G>T	uc010njr.1	-	9	1578	c.1518C>A	c.(1516-1518)ATC>ATA	p.I506I		NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa	506	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)					GGAGGAAGACGATCCCCTGAT	0.448													18	16	---	---	---	---	PASS
MTMR8	55613	broad.mit.edu	37	X	63574825	63574825	+	Intron	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63574825G>C	uc004dvs.2	-						MTMR8_uc011mou.1_Intron|MTMR8_uc004dvt.1_Intron	NM_017677	NP_060147	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8							nuclear envelope	protein tyrosine phosphatase activity			ovary(2)|breast(2)	4						CTGGAGAAGAGAGATAGGCAT	0.348													5	4	---	---	---	---	PASS
XIST	7503	broad.mit.edu	37	X	73069027	73069027	+	RNA	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73069027G>C	uc004ebm.1	-	1		c.3562C>G				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0						TTACTACTTTGTTCTTTAATT	0.433													15	11	---	---	---	---	PASS
RPS6KA6	27330	broad.mit.edu	37	X	83352865	83352865	+	Intron	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83352865G>C	uc004eej.1	-						RPS6KA6_uc011mqt.1_Intron|RPS6KA6_uc011mqu.1_Intron	NM_014496	NP_055311	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase polypeptide 6						axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|central_nervous_system(1)|skin(1)	8						ACCTAAGAAAGAAATACTCAT	0.308													23	19	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91132500	91132500	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91132500G>T	uc004efk.1	+	2	2106	c.1261G>T	c.(1261-1263)GCA>TCA	p.A421S	PCDH11X_uc004efl.1_Missense_Mutation_p.A421S|PCDH11X_uc004efo.1_Missense_Mutation_p.A421S|PCDH11X_uc010nmv.1_Missense_Mutation_p.A421S|PCDH11X_uc004efm.1_Missense_Mutation_p.A421S|PCDH11X_uc004efn.1_Missense_Mutation_p.A421S|PCDH11X_uc004efh.1_Missense_Mutation_p.A421S|PCDH11X_uc004efj.1_Missense_Mutation_p.A421S	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	421	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						CCTGGAGACTGCAGCATATCT	0.433													22	25	---	---	---	---	PASS
DRP2	1821	broad.mit.edu	37	X	100503557	100503557	+	Missense_Mutation	SNP	G	C	C	rs149294275	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100503557G>C	uc004egz.2	+	14	1878	c.1509G>C	c.(1507-1509)TTG>TTC	p.L503F	DRP2_uc011mrh.1_Missense_Mutation_p.L425F	NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	503					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2						TTGCATGCTTGTGTGGCACGG	0.468													58	58	---	---	---	---	PASS
VGLL1	51442	broad.mit.edu	37	X	135631089	135631089	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135631089G>A	uc004ezy.2	+	3	726	c.556G>A	c.(556-558)GCC>ACC	p.A186T	MIR934_hsa-mir-934|MI0005756_5'Flank	NM_016267	NP_057351	Q99990	VGLL1_HUMAN	vestigial like 1	186					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription coactivator activity				0	Acute lymphoblastic leukemia(192;0.000127)					GGAATCTGCCGCCAGGGAGAA	0.577													38	23	---	---	---	---	PASS
FMR1	2332	broad.mit.edu	37	X	147030327	147030327	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147030327T>A	uc010nst.2	+	17	2051	c.1862T>A	c.(1861-1863)GTG>GAG	p.V621E	FMR1_uc004fcj.2_Missense_Mutation_p.V581E|FMR1_uc004fck.3_Missense_Mutation_p.V575E|FMR1_uc004fcl.3_Missense_Mutation_p.V461E|FMR1_uc011mxa.1_Missense_Mutation_p.V251E	NM_002024	NP_002015	Q06787	FMR1_HUMAN	fragile X mental retardation 1	621	Interaction with RANBP9.				mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGACAGCGTGGATGGTCAG	0.423									Fragile_X_syndrome				27	23	---	---	---	---	PASS
CNGA2	1260	broad.mit.edu	37	X	150912443	150912443	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150912443G>C	uc004fey.1	+	7	1692	c.1468G>C	c.(1468-1470)GAG>CAG	p.E490Q		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	490	cAMP (By similarity).|Cytoplasmic (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					catcggcaaGGAGATGTACAT	0.423													35	35	---	---	---	---	PASS
RBMY1A1	5940	broad.mit.edu	37	Y	23702602	23702602	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:23702602C>A	uc004fuq.3	+	4	444	c.332C>A	c.(331-333)TCT>TAT	p.S111Y	RBMY1A1_uc010nxa.2_Missense_Mutation_p.S111Y|RBMY1A1_uc004fur.3_Intron|RBMY1A1_uc011nbd.1_Missense_Mutation_p.S76Y	NM_001006120	NP_001006120	Q15414	RBY1A_HUMAN	RNA binding motif protein, Y-linked, family 1,	111					mRNA processing|RNA splicing|spermatogenesis	nucleus	nucleotide binding|RNA binding				0						AGTCTGAGATCTGCAAGAGGA	0.458													8	70	---	---	---	---	PASS
MIB2	142678	broad.mit.edu	37	1	1564953	1564953	+	Intron	DEL	G	-	-	rs112177324		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1564953delG	uc001agg.2	+						MIB2_uc001agh.2_Intron|MIB2_uc001agi.2_Intron|MIB2_uc001agj.2_Intron|MIB2_uc001agk.2_Intron|MIB2_uc001agm.2_Intron|MIB2_uc010nyq.1_Intron|MIB2_uc009vkh.2_Intron|MIB2_uc001agn.2_Intron|MIB2_uc001ago.2_Intron|MMP23B_uc001agp.2_5'Flank|MMP23B_uc001agq.2_5'Flank	NM_080875	NP_543151	Q96AX9	MIB2_HUMAN	mindbomb homolog 2						Notch signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade	endosome	actin binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GAGGGTGAGTGGGGGGCCCCG	0.716													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2372020	2372020	+	IGR	DEL	T	-	-	rs77708992		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2372020delT								PEX10 (28010 upstream) : PLCH2 (35734 downstream)																							GGATCTTGCATTGCTGCGACC	0.657													5	3	---	---	---	---	
TP73	7161	broad.mit.edu	37	1	3628411	3628412	+	Intron	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3628411_3628412delTG	uc001akp.2	+						TP73_uc001akq.2_Intron|TP73_uc010nzj.1_Intron|TP73_uc001akr.2_Intron|TP73_uc009vlk.1_Intron|TP73_uc001aks.2_Intron|TP73_uc010nzk.1_Intron	NM_005427	NP_005418	O15350	P73_HUMAN	tumor protein p73 isoform a						cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|protein tetramerization|response to gamma radiation|response to X-ray	chromatin|cytosol|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)		agcgtgtgtatgtgtgtgtgtg	0.470													4	2	---	---	---	---	
LRRC47	57470	broad.mit.edu	37	1	3701558	3701558	+	Intron	DEL	A	-	-	rs34940702		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3701558delA	uc001akx.1	-							NM_020710	NP_065761	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47						translation		phenylalanine-tRNA ligase activity|RNA binding			large_intestine(1)|ovary(1)	2	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		ctccatctccaaaaaaaaaaa	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5342964	5342965	+	IGR	INS	-	G	G	rs145826888	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5342964_5342965insG								AJAP1 (499114 upstream) : NPHP4 (579905 downstream)																							TGGCCAGAGCAGGGGGCTGGGG	0.589													6	5	---	---	---	---	
PEX14	5195	broad.mit.edu	37	1	10651692	10651693	+	Intron	INS	-	TG	TG	rs149399513	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10651692_10651693insTG	uc001arn.2	+						PEX14_uc009vmu.1_Intron|PEX14_uc009vmv.2_Intron|PEX14_uc010oam.1_Intron|PEX14_uc010oan.1_Intron|PEX14_uc009vmw.2_Intron	NM_004565	NP_004556	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14						negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|protein homooligomerization|protein import into peroxisome matrix|transmembrane transport	integral to membrane|nucleus|peroxisomal membrane|protein complex	protein N-terminus binding|transcription corepressor activity			breast(1)	1	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		GGTATACACACtgtgtgtgtgt	0.361													4	2	---	---	---	---	
TNFRSF1B	7133	broad.mit.edu	37	1	12248241	12248242	+	Intron	DEL	TG	-	-	rs3216795		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12248241_12248242delTG	uc001att.2	+						TNFRSF1B_uc001atu.2_Intron|TNFRSF1B_uc009vnk.2_Intron	NM_001066	NP_001057	P20333	TNR1B_HUMAN	tumor necrosis factor receptor 2 precursor						apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity			liver(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)|Infliximab(DB00065)	CTGCATCACATGAGTGTGTGTG	0.381													3	4	---	---	---	---	
VPS13D	55187	broad.mit.edu	37	1	12316747	12316748	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12316747_12316748insT	uc001atv.2	+						VPS13D_uc001atw.2_Intron	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TCTCAGGTTAGttttttttttt	0.317													4	3	---	---	---	---	
AADACL3	126767	broad.mit.edu	37	1	12774618	12774618	+	5'Flank	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12774618delA	uc009vnn.1	+						AADACL3_uc001aug.1_5'Flank	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1								hydrolase activity				0	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		cccatctcagaaaaaaaaaaa	0.179													3	4	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16965449	16965449	+	Intron	DEL	A	-	-	rs141730973		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16965449delA	uc001azg.1	-						CROCCL1_uc001azi.1_Intron|uc001azj.1_Intron					Homo sapiens mRNA for FLJ00313 protein.												0						cctgcctcttaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17015710	17015710	+	IGR	DEL	T	-	-	rs112604834		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17015710delT								MST1P2 (38796 upstream) : ESPNP (2003 downstream)																							acccagctaattttttttttt	0.000													4	2	---	---	---	---	
IGSF21	84966	broad.mit.edu	37	1	18627815	18627818	+	Intron	DEL	TTTG	-	-	rs111517891		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18627815_18627818delTTTG	uc001bau.1	+							NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor							extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		TGGTAATTGTtttgtttgtttgtt	0.206													3	3	---	---	---	---	
AKR7L	246181	broad.mit.edu	37	1	19593410	19593411	+	3'UTR	DEL	CT	-	-	rs57351921		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19593410_19593411delCT	uc010ocx.1	-	8					AKR7L_uc010ocy.1_3'UTR	NM_201252	NP_957704			aflatoxin B1 aldehyde reductase 3 isoform 1												0						ATTTcctcccctgtctgtctct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20687589	20687596	+	IGR	DEL	TGTGTGTG	-	-	rs72051604		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20687589_20687596delTGTGTGTG								VWA5B1 (6202 upstream) : CAMK2N1 (121289 downstream)																							AGGCCAGTTTtgtgtgtgtgtgtgtgtg	0.365													4	2	---	---	---	---	
ZBTB40	9923	broad.mit.edu	37	1	22841697	22841697	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22841697delT	uc001bft.2	+						ZBTB40_uc001bfu.2_Intron|ZBTB40_uc009vqi.1_Intron	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40						bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		ggaaacgagctttacctgcat	0.000													4	2	---	---	---	---	
C1QC	714	broad.mit.edu	37	1	22967712	22967713	+	5'Flank	DEL	CG	-	-	rs6691043	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22967712_22967713delCG	uc001bgc.3	+						C1QC_uc001bga.3_5'Flank|C1QC_uc001bgb.2_5'Flank	NM_172369	NP_758957	P02747	C1QC_HUMAN	complement component 1, q subcomponent, C chain						complement activation, classical pathway|innate immune response|negative regulation of granulocyte differentiation|negative regulation of macrophage differentiation	collagen					0		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.21e-27)|Colorectal(126;1.5e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.61e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000538)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.196)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	cacacacacacgcacacacCAG	0.431													4	2	---	---	---	---	
FUCA1	2517	broad.mit.edu	37	1	24195739	24195741	+	5'Flank	DEL	AGG	-	-	rs72087827		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24195739_24195741delAGG	uc001bie.2	-						FUCA1_uc009vqt.1_5'Flank|FUCA1_uc010oed.1_5'Flank	NM_000147	NP_000138	P04066	FUCO_HUMAN	fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		gaaggaaggaaggaggaaggaag	0.232													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30879662	30879665	+	IGR	DEL	ACAC	-	-	rs145269855		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30879662_30879665delACAC								None (None upstream) : MATN1 (304461 downstream)																							GGAGTGAGAAacacacacacacac	0.426													4	2	---	---	---	---	
S100PBP	64766	broad.mit.edu	37	1	33296522	33296522	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33296522delA	uc001bvz.2	+						S100PBP_uc001bwa.1_Intron|S100PBP_uc001bwb.1_Intron|S100PBP_uc001bwc.2_Intron|S100PBP_uc001bwd.2_Intron	NM_022753	NP_073590	Q96BU1	S1PBP_HUMAN	S100P binding protein isoform a							nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				ttcttttgggaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35180287	35180288	+	IGR	DEL	CT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35180287_35180288delCT								MIR552 (44992 upstream) : GJB5 (40433 downstream)																							cacccagcagctctctctctct	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37154585	37154588	+	IGR	DEL	GGAA	-	-	rs111279905		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37154585_37154588delGGAA								CSF3R (206076 upstream) : GRIK3 (106540 downstream)																							tgtgggaaggggaaggAAGGGGAA	0.113													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	40298569	40298574	+	IGR	DEL	GACCAC	-	-	rs67546362		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40298569_40298574delGACCAC								BMP8B (44036 upstream) : TRIT1 (8134 downstream)																							AGCTTCCAATGACCACGACCACGTGA	0.481													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	43496658	43496659	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43496658_43496659insT								SLC2A1 (71811 upstream) : FAM183A (116935 downstream)																							tgggaaatttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48209048	48209049	+	IGR	INS	-	TGC	TGC			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48209048_48209049insTGC								FOXD2 (302686 upstream) : SKINTL (358338 downstream)																							ggtggtagtggtggtggtggtg	0.000													4	2	---	---	---	---	
SLC1A7	6512	broad.mit.edu	37	1	53586230	53586230	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53586230delT	uc001cuy.2	-						SLC1A7_uc001cuz.3_Intron	NM_006671	NP_006662	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter),							integral to membrane|plasma membrane	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|large_intestine(1)	3				Colorectal(1306;0.234)	L-Glutamic Acid(DB00142)	tcctcccgcctggaactctcc	0.219													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58825354	58825355	+	Intron	INS	-	GATGATAGCAAGGGGTGAGAGT	GATGATAGCAAGGGGTGAGAGT	rs145013673	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58825354_58825355insGATGATAGCAAGGGGTGAGAGT	uc001cyt.1	-							NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						TGATAGGTAGAGATGATAGCAA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62656920	62656921	+	IGR	INS	-	TT	TT	rs145762114		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62656920_62656921insTT								INADL (12574 upstream) : L1TD1 (3575 downstream)																							CTCTTTCATAAttttttttttt	0.228													4	2	---	---	---	---	
RAVER2	55225	broad.mit.edu	37	1	65274936	65274937	+	Intron	DEL	TT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65274936_65274937delTT	uc001dbs.1	+						RAVER2_uc001dbt.1_Intron|RAVER2_uc010opb.1_Intron	NM_018211	NP_060681	Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2							cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)	1						ccaaaagcaattaagcagagcc	0.000													3	3	---	---	---	---	
JAK1	3716	broad.mit.edu	37	1	65366126	65366126	+	Intron	DEL	G	-	-	rs56353233		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65366126delG	uc001dbu.1	-						JAK1_uc009wam.1_Intron	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		CAAGACTTAAGCATTTCATGA	0.438			Mis		ALL								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	65560049	65560049	+	IGR	DEL	T	-	-	rs112247383		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65560049delT								MIR101-1 (35858 upstream) : AK3L1 (53183 downstream)																							cagttggttgttaagtatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	66164156	66164156	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66164156delA								LEPR (61336 upstream) : PDE4B (94037 downstream)																							CTTTTTACTTAAAAAAAAAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	66842311	66842311	+	IGR	DEL	C	-	-	rs68069761		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66842311delC								PDE4B (2050 upstream) : SGIP1 (157514 downstream)																							ACAAGTAGAACCCTTTTTATT	0.279													3	3	---	---	---	---	
SLC35D1	23169	broad.mit.edu	37	1	67474031	67474031	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67474031delA	uc001ddk.2	-						SLC35D1_uc010oph.1_3'UTR	NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic						chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	catgttggccagggtggtctt	0.114													4	2	---	---	---	---	
IL12RB2	3595	broad.mit.edu	37	1	67833171	67833174	+	Intron	DEL	CAAA	-	-	rs113892136	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67833171_67833174delCAAA	uc001ddu.2	+						IL12RB2_uc010oqi.1_Intron|IL12RB2_uc010oqj.1_Intron|IL12RB2_uc010oqk.1_Intron|IL12RB2_uc010oql.1_Intron|IL12RB2_uc010oqm.1_Intron|IL12RB2_uc010oqn.1_Intron	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor						positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3						aggaaggaagcaaagaaggaagga	0.059													4	2	---	---	---	---	
IL12RB2	3595	broad.mit.edu	37	1	67856684	67856685	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67856684_67856685insA	uc001ddu.2	+						IL12RB2_uc010oqi.1_Intron|IL12RB2_uc010oqj.1_Intron|IL12RB2_uc010oqk.1_Intron|IL12RB2_uc010oql.1_Intron|IL12RB2_uc010oqm.1_Intron|IL12RB2_uc010oqn.1_Intron	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor						positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3						AACCTCCACTCAAAAAAAAAGA	0.381													4	2	---	---	---	---	
ANKRD13C	81573	broad.mit.edu	37	1	70747260	70747260	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70747260delT	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0						ttgtttttactttttttttgt	0.000													4	2	---	---	---	---	
C1orf173	127254	broad.mit.edu	37	1	75039507	75039507	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75039507delA	uc001dgg.2	-							NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						TGGAATCAGCAAAAtctccac	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	80250285	80250286	+	IGR	INS	-	TTT	TTT	rs66477173		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80250285_80250286insTTT								ELTD1 (777790 upstream) : None (None downstream)																							TTTTGCCATGCTTTTTTTTTTT	0.386													6	5	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82370784	82370785	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82370784_82370785insT	uc001dit.3	+						LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Intron|LPHN2_uc001div.2_Intron|LPHN2_uc009wcd.2_Intron	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		CCTTACTATACttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	85226945	85226947	+	IGR	DEL	AAT	-	-	rs75565894		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85226945_85226947delAAT								SSX2IP (70505 upstream) : LPAR3 (52139 downstream)																							taacaacaacaataaAATGACCA	0.365													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88124715	88124716	+	IGR	INS	-	GT	GT	rs140238963	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88124715_88124716insGT								LMO4 (310112 upstream) : None (None downstream)																							tgtgtgtgtgcgtgtgtgtatg	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	99818213	99818214	+	IGR	INS	-	G	G	rs150555875	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99818213_99818214insG								LPPR4 (43077 upstream) : PALMD (293217 downstream)																							TGTTTTGCCTTGCAATTAAATT	0.262													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	108060787	108060788	+	IGR	INS	-	A	A	rs150051629		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108060787_108060788insA								NTNG1 (36316 upstream) : VAV3 (52994 downstream)																							TCACTGGCAAGAAAAAAAAAAa	0.193													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	113687568	113687569	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113687568_113687569insT								LRIG2 (20226 upstream) : MAGI3 (245906 downstream)																							TCATGATCCACttttttttttt	0.188													4	2	---	---	---	---	
DENND2C	163259	broad.mit.edu	37	1	115092121	115092122	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115092121_115092122insT	uc001eez.2	-							NM_198459		Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C											skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAATTTCGttcttttttttttt	0.168													4	3	---	---	---	---	
IGSF3	3321	broad.mit.edu	37	1	117137539	117137540	+	Intron	INS	-	G	G	rs143026687		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117137539_117137540insG	uc001egr.1	-						IGSF3_uc001egq.1_Intron|IGSF3_uc001egs.1_Intron	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2							integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		CCCCCTGCCCCCGTTCATGCCC	0.589													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142576687	142576687	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142576687delC								None (None upstream) : None (None downstream)																							CTACACTTCACAGCATTCAAA	0.378													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143534375	143534376	+	IGR	INS	-	C	C	rs151315332		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143534375_143534376insC								None (None upstream) : LOC100286793 (113263 downstream)																							ggagatagcatagatcccaaaa	0.000													2	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144853333	144853334	+	Intron	INS	-	AA	AA	rs149112816		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144853333_144853334insAA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGTGAAAAAATAAAAAAAAGAG	0.356			T	PDGFRB	MPD								3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145033613	145033614	+	Intron	INS	-	AAA	AAA	rs141798859		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145033613_145033614insAAA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAAACAAAGTCAAAATTCTTAA	0.327			T	PDGFRB	MPD								3	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145106430	145106439	+	Intron	DEL	TGTGTGTGTA	-	-	rs3977180		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145106430_145106439delTGTGTGTGTA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						tattccatggtgtgtgtgtatgtgtgtgtg	0.000													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145112003	145112003	+	Intron	DEL	G	-	-	rs4247156		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145112003delG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TGGtttttttgtttttgtttt	0.169													5	4	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145993328	145993329	+	Intron	INS	-	AGAA	AGAA	rs138474935	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145993328_145993329insAGAA	uc001emp.3	+							NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ttaactttattagaaactatca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148868452	148868453	+	IGR	INS	-	T	T	rs149506016		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148868452_148868453insT								NBPF16 (110141 upstream) : LOC645166 (59833 downstream)																							ATAAAAACTCCttttttttttt	0.158													4	2	---	---	---	---	
LOC645166	645166	broad.mit.edu	37	1	148948880	148948881	+	Intron	INS	-	A	A	rs144249846		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148948880_148948881insA	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0						caagactatctaaaaaaaaaaa	0.124													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149237008	149237009	+	IGR	INS	-	C	C	rs150330745	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149237008_149237009insC								LOC645166 (283954 upstream) : LOC388692 (42467 downstream)																							ttcctttagtttttgggtacct	0.000													4	3	---	---	---	---	
MRPS21	54460	broad.mit.edu	37	1	150269271	150269271	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150269271delA	uc001euk.2	+						MRPS21_uc001eul.2_Intron	NM_031901	NP_114107	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome				0	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTGTCGCTTTAAAAAAAAAAC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	150542471	150542471	+	IGR	DEL	A	-	-	rs11285885		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150542471delA								ADAMTSL4 (9061 upstream) : MCL1 (4566 downstream)																							acctcgggtgatctacccacc	0.070													3	3	---	---	---	---	
LYSMD1	388695	broad.mit.edu	37	1	151133973	151133973	+	Intron	DEL	A	-	-	rs33999172		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151133973delA	uc001ewy.2	-						LYSMD1_uc010pcr.1_Intron	NM_212551	NP_997716	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain						cell wall macromolecule catabolic process						0	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			accccgtctcaaaaaaaaaaa	0.209													2	4	---	---	---	---	
PGLYRP4	57115	broad.mit.edu	37	1	153308522	153308527	+	Intron	DEL	GTGTGT	-	-	rs112779198		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153308522_153308527delGTGTGT	uc001fbo.2	-						PGLYRP4_uc001fbp.2_Intron	NM_020393	NP_065126	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein-I-beta						defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)|skin(1)	4	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			gggtgcgtgcgtgtgtgtgtgtgtgt	0.000													4	3	---	---	---	---	
ADAR	103	broad.mit.edu	37	1	154556762	154556763	+	3'UTR	DEL	CT	-	-	rs71774557		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154556762_154556763delCT	uc001ffh.2	-	15					ADAR_uc001ffj.2_3'UTR|ADAR_uc001ffi.2_3'UTR|ADAR_uc001ffk.2_3'UTR	NM_001111	NP_001102	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform a						adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TTATGTTCACCTCTTTGCCCTC	0.470													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158855906	158855906	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158855906delA								MNDA (36636 upstream) : PYHIN1 (45436 downstream)																							aggaggagccaagatggccga	0.169													2	4	---	---	---	---	
CD84	8832	broad.mit.edu	37	1	160517850	160517850	+	3'UTR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160517850delA	uc001fwh.3	-	8					CD84_uc001fwf.3_3'UTR|CD84_uc001fwg.3_3'UTR|CD84_uc009wtn.2_3'UTR|CD84_uc001fwi.3_3'UTR	NM_003874	NP_003865	Q9UIB8	SLAF5_HUMAN	CD84 molecule						blood coagulation|defense response|homophilic cell adhesion|leukocyte migration	integral to plasma membrane	receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GAGTCATTTCAGGAAGGGTAT	0.338													4	2	---	---	---	---	
FCGR2B	2213	broad.mit.edu	37	1	161646661	161646661	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161646661delC	uc001gaz.1	+						FCGR2B_uc001gay.1_Intron|FCGR2B_uc001gba.1_Intron|FCGR2B_uc001gbb.1_Intron|FCGR2B_uc009wun.1_Intron	NM_004001	NP_003992	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor						immune response|interspecies interaction between organisms|regulation of immune response	integral to membrane|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCATGGAGTACCATATTTTTC	0.303			T	?	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	162458538	162458539	+	IGR	INS	-	T	T	rs6699463	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162458538_162458539insT								SH2D1B (76610 upstream) : UHMK1 (8425 downstream)																							TTCTAtttctgttttttttttt	0.218													3	3	---	---	---	---	
LMX1A	4009	broad.mit.edu	37	1	165181473	165181488	+	Intron	DEL	ACGCTGGGCTAAGCCC	-	-	rs11269295		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165181473_165181488delACGCTGGGCTAAGCCC	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron|LMX1A_uc001gcw.1_Intron|LMX1A_uc001gcx.1_Intron	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)					CACTGCACCTACGCTGGGCTAAGCCCATGCCTTGCT	0.514													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168706271	168706272	+	IGR	INS	-	T	T	rs143217918	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168706271_168706272insT								DPT (7843 upstream) : MGC4473 (49907 downstream)																							ggaagctgccatttttttttag	0.000													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	171807693	171807693	+	5'Flank	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171807693delA	uc001gie.2	+						DNM3_uc001gid.3_5'Flank|DNM3_uc009wwb.2_5'Flank|DNM3_uc001gif.2_5'Flank	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						aatacgaaacaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172963949	172963949	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172963949delG								FASLG (327939 upstream) : TNFSF18 (46411 downstream)																							CTTTAGGCCAGGGAAGGTAAC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	176819234	176819234	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176819234delC								PAPPA2 (7266 upstream) : ASTN1 (7207 downstream)																							aggatttggacccagtagtct	0.179													4	2	---	---	---	---	
ASTN1	460	broad.mit.edu	37	1	176926497	176926500	+	Intron	DEL	TAGG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176926497_176926500delTAGG	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						ACTCTAGCTTTAGGTAGGTTTCTC	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178012452	178012452	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178012452delA								SEC16B (5310 upstream) : LOC100302401 (48191 downstream)																							ccattaggctaagcaaattac	0.000													4	2	---	---	---	---	
FAM163A	148753	broad.mit.edu	37	1	179762151	179762151	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179762151delA	uc009wxj.2	+						FAM163A_uc001gnj.2_Intron|FAM163A_uc009wxk.2_Intron	NM_173509	NP_775780	Q96GL9	F163A_HUMAN	hypothetical protein LOC148753							integral to membrane				ovary(1)	1						GAATATCATGAAAAAAAAAAG	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181966856	181966856	+	IGR	DEL	A	-	-	rs35291731		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181966856delA								CACNA1E (196143 upstream) : ZNF648 (56851 downstream)																							tatttagcagatgtaatccag	0.000													4	2	---	---	---	---	
SOX13	9580	broad.mit.edu	37	1	204081629	204081630	+	Intron	INS	-	CA	CA	rs6143576		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204081629_204081630insCA	uc001ham.2	+						SOX13_uc001hal.2_Intron|SOX13_uc010pqp.1_5'Flank	NM_005686	NP_005677	Q9UN79	SOX13_HUMAN	SRY-box 13						anatomical structure morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			acacatgcgtgcacacacacac	0.203													4	3	---	---	---	---	
LGTN	1939	broad.mit.edu	37	1	206770284	206770284	+	Intron	DEL	C	-	-	rs138836612		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206770284delC	uc001heh.2	-						LGTN_uc009xbw.2_Intron	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin						intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			GTTCCAAAGACCCCCCCAAAT	0.313													6	4	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207087754	207087757	+	Intron	DEL	TTCC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207087754_207087757delTTCC	uc001hey.2	-						FAIM3_uc010prz.1_Intron|FAIM3_uc010psa.1_Intron|FAIM3_uc010psb.1_Intron	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					ctttctttctttccttccttcctt	0.000													3	3	---	---	---	---	
PTPN14	5784	broad.mit.edu	37	1	214638195	214638196	+	5'UTR	DEL	CT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214638195_214638196delCT	uc001hkk.1	-	2					PTPN14_uc010pty.1_Intron	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GCACACGCCCCTGAGATGGCCT	0.599													22	12	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	216363840	216363841	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216363840_216363841insT	uc001hku.1	-						USH2A_uc001hkv.2_Intron	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TAGGAAAAGGGTTTTTTTTTTT	0.337										HNSCC(13;0.011)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	219409164	219409164	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219409164delG								LYPLAL1 (22958 upstream) : SLC30A10 (449605 downstream)																							GTGCATTTTTGTAAGGAGCCC	0.393													4	2	---	---	---	---	
CAPN8	388743	broad.mit.edu	37	1	223821096	223821097	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223821096_223821097insA	uc009xee.2	-							NM_001143962	NP_001137434	A6NHC0	CAN8_HUMAN	calpain 8						proteolysis	Golgi apparatus	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0						AATGCTCTCTTAAAAAAAAAAA	0.238													3	3	---	---	---	---	
DEGS1	8560	broad.mit.edu	37	1	224370132	224370133	+	5'Flank	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224370132_224370133delTG	uc001hoj.2	+						DEGS1_uc001hoi.2_Intron	NM_144780	NP_659004	O15121	DEGS1_HUMAN	degenerative spermatocyte homolog 1, lipid						sphingolipid metabolic process|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	electron carrier activity|protein binding|sphingolipid delta-4 desaturase activity				0	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		cgatcagattTGTGTGTGTGTG	0.228													4	2	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230296470	230296470	+	Intron	DEL	C	-	-	rs4846915	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230296470delC	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				aaaaaaaaaaCACGAAACTTT	0.214													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	233078330	233078332	+	IGR	DEL	GAA	-	-	rs10545871		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233078330_233078332delGAA								KIAA1383 (132238 upstream) : C1orf57 (8038 downstream)																							aaggagggaggaaggaaggagaa	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	234918511	234918512	+	IGR	INS	-	GT	GT	rs146753231		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234918511_234918512insGT								IRF2BP2 (173240 upstream) : TOMM20 (354148 downstream)																							TGGTTTTTGTAGTGTGTGTGTG	0.401													5	3	---	---	---	---	
GNG4	2786	broad.mit.edu	37	1	235779933	235779933	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235779933delC	uc001hxe.3	-						GNG4_uc009xfz.2_Intron|GNG4_uc001hxh.3_Intron	NM_001098722	NP_001092192	P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|negative regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			ACCTCCTTTTCTCTCTGTGAC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236247168	236247169	+	IGR	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236247168_236247169insA								NID1 (18687 upstream) : GPR137B (58663 downstream)																							CAGGGCGAGGGATGTGCTTTCT	0.500													4	2	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236709074	236709075	+	Intron	INS	-	G	G	rs140571553	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236709074_236709075insG	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GAAGGTTCCCTGAAGTTGTGGA	0.426													3	3	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237642744	237642744	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237642744delT	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTGGTTTGTCTTTATACTGCA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238704321	238704322	+	IGR	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238704321_238704322delGT								LOC339535 (55004 upstream) : CHRM3 (845543 downstream)																							GTGCACCCACGTGTGTGTGTGA	0.421													4	2	---	---	---	---	
CHRM3	1131	broad.mit.edu	37	1	239748833	239748833	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239748833delG	uc001hyo.1	+									P20309	ACM3_HUMAN	Homo sapiens clone N10 NTera2D1 teratocarcinoma, m3 muscarinic acetylcholine receptor mRNA, partial cds.						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)	TTGTCATAAAGGGCAACCGTC	0.463													4	2	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	240991387	240991387	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240991387delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron|RGS7_uc001hyt.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			AGAAACTGGTAAATAAGATGC	0.413													4	2	---	---	---	---	
KMO	8564	broad.mit.edu	37	1	241728737	241728737	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241728737delG	uc009xgp.2	+						KMO_uc001hyy.2_Intron|KMO_uc009xgo.1_Intron	NM_003679	NP_003670	O15229	KMO_HUMAN	kynurenine 3-monooxygenase						pyridine nucleotide biosynthetic process|response to salt stress	cytosol|integral to membrane|mitochondrial outer membrane	electron carrier activity|flavin adenine dinucleotide binding|kynurenine 3-monooxygenase activity|NAD(P)H oxidase activity			ovary(2)	2	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			aagagagcatggGGATgggcg	0.010													4	2	---	---	---	---	
EXO1	9156	broad.mit.edu	37	1	242051712	242051715	+	Intron	DEL	CTGT	-	-	rs140295406		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242051712_242051715delCTGT	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			tgtgatgccactgtcttgattcac	0.000								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244145746	244145746	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244145746delT	uc001iac.2	+											Homo sapiens cDNA clone IMAGE:5244187.																		ttggaggctattaattgtgct	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244456438	244456439	+	IGR	INS	-	T	T	rs35987524		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244456438_244456439insT								ZNF238 (235662 upstream) : C1orf100 (59498 downstream)																							caaagagtggattttttttttt	0.000													2	4	---	---	---	---	
SH3YL1	26751	broad.mit.edu	37	2	244569	244572	+	Intron	DEL	AAAG	-	-	rs67069906		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:244569_244572delAAAG	uc002qvx.2	-						SH3YL1_uc002qvy.2_Intron|SH3YL1_uc002qvz.2_Intron|SH3YL1_uc002qwa.2_Intron|SH3YL1_uc010ewe.2_Intron|SH3YL1_uc002qwc.1_Intron|SH3YL1_uc002qvu.2_Intron|SH3YL1_uc002qvv.2_Intron|SH3YL1_uc002qvw.2_Intron|uc002qwb.2_5'Flank	NM_015677	NP_056492	Q96HL8	SH3Y1_HUMAN	SH3 domain containing, Ysc84-like 1 isoform 1											ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		aagaaaagaaaaagaaagaaagaa	0.132													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	748123	748125	+	IGR	DEL	ACT	-	-	rs111389563		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:748123_748125delACT								TMEM18 (70684 upstream) : SNTG2 (198430 downstream)																							cctcaccatcactaccaccaatg	0.153													4	2	---	---	---	---	
TPO	7173	broad.mit.edu	37	2	1402976	1402976	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1402976delC	uc010ewj.2	+									P07202	PERT_HUMAN	Homo sapiens mRNA for thyroid peroxidase isoform d variant protein.						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	AAATGTCCAGCCCCCCCGAGG	0.597													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10981603	10981604	+	IGR	INS	-	AG	AG	rs141068983	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10981603_10981604insAG								PDIA6 (3500 upstream) : KCNF1 (70459 downstream)																							cctgaaaactcagagagagaga	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11040910	11040910	+	IGR	DEL	A	-	-	rs113522289		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11040910delA								PDIA6 (62807 upstream) : KCNF1 (11153 downstream)																							ggccctgagcaaaggacccag	0.000													4	3	---	---	---	---	
GREB1	9687	broad.mit.edu	37	2	11734814	11734815	+	Intron	INS	-	TTG	TTG	rs146182180	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11734814_11734815insTTG	uc002rbk.1	+						GREB1_uc002rbo.1_Intron	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TTCTGTGttttttgttgttgtt	0.054													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12031560	12031560	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12031560delT								LPIN1 (64029 upstream) : TRIB2 (825438 downstream)																							CAAGAGGCGCTTTTTTTTTTT	0.348													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12691932	12691932	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12691932delT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		aagctttttcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15066609	15066609	+	IGR	DEL	G	-	-	rs5829481		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15066609delG								FAM84A (275676 upstream) : NBAS (240423 downstream)																							CATTTCAGCTGGTACTTGTGT	0.358													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17342691	17342691	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17342691delC								FAM49A (495595 upstream) : RAD51AP2 (349295 downstream)																							CGAATGTCTGCCCCCTGACAC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19068438	19068439	+	IGR	INS	-	TG	TG	rs113096673		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19068438_19068439insTG								NT5C1B (297600 upstream) : OSR1 (482808 downstream)																							CAGGATTCAGAtgtgtgtgtgt	0.252													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19563563	19563563	+	IGR	DEL	T	-	-	rs33929093		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19563563delT								OSR1 (5191 upstream) : TTC32 (532955 downstream)																							TGCTGCTTCCTTTTTTTTTTT	0.438													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20006969	20006969	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20006969delA								OSR1 (448597 upstream) : TTC32 (89549 downstream)																							CCTTATTTTTAAAAAGGGACC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20672872	20672873	+	IGR	INS	-	C	C	rs149400603	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20672872_20672873insC								RHOB (23672 upstream) : HS1BP3 (144691 downstream)																							ccagcttcccatgaagggtact	0.114													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21082713	21082714	+	IGR	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21082713_21082714delGT								C2orf43 (59886 upstream) : APOB (141588 downstream)																							GCCCAGCCTGGTGTGTGTGTGT	0.391													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23157748	23157749	+	IGR	DEL	AG	-	-	rs138717007		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23157748_23157749delAG								None (None upstream) : KLHL29 (597706 downstream)																							tcatatcaacagagtttttgat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23588036	23588039	+	IGR	DEL	AGAG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23588036_23588039delAGAG								None (None upstream) : KLHL29 (167416 downstream)																							cttgaaggaaagagagagagagag	0.069													4	2	---	---	---	---	
ATAD2B	54454	broad.mit.edu	37	2	24084019	24084020	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24084019_24084020insT	uc002rek.3	-						ATAD2B_uc010yki.1_Intron	NM_017552	NP_060022	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTTTTTTTCCTTTTTTTTTTT	0.144													3	3	---	---	---	---	
C2orf44	80304	broad.mit.edu	37	2	24254696	24254696	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24254696delA	uc002rep.2	-						C2orf44_uc010eya.2_Intron	NM_025203	NP_079479	Q9H6R7	CB044_HUMAN	hypothetical protein LOC80304 isoform 1								protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					actcggtctcaaaaaaaaaaa	0.090													3	3	---	---	---	---	
LOC375190	375190	broad.mit.edu	37	2	24382860	24382860	+	Intron	DEL	T	-	-	rs71397412		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24382860delT	uc010ykl.1	+						LOC375190_uc002rew.2_Intron|LOC375190_uc002rfb.2_Intron	NM_001145710	NP_001139182			hypothetical protein LOC375190												0						tttcttttcattttttttttt	0.000													8	4	---	---	---	---	
ADCY3	109	broad.mit.edu	37	2	25046362	25046362	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25046362delT	uc002rfs.3	-						ADCY3_uc002rfr.3_Intron|ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TATTCCAGCAttttttttttt	0.219													5	3	---	---	---	---	
ADCY3	109	broad.mit.edu	37	2	25115122	25115123	+	Intron	INS	-	T	T	rs113869582		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25115122_25115123insT	uc002rfs.3	-						ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					tgtattgagtcttttttttttt	0.000													2	4	---	---	---	---	
OTOF	9381	broad.mit.edu	37	2	26751202	26751202	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26751202delT	uc002rhk.2	-							NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a						cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTGAGCCTGGTTTTTGGTGGG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	29196319	29196320	+	IGR	INS	-	CCCTTCC	CCCTTCC	rs143947941	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29196319_29196320insCCCTTCC								WDR43 (25239 upstream) : FAM179A (7844 downstream)																							cttccttccttccttccttcct	0.015													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29487874	29487874	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29487874delT	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GGGTGCCCTGttttttttttg	0.065			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29676067	29676068	+	Intron	INS	-	CAA	CAA	rs143440327	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29676067_29676068insCAA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	tactgtttttgcaactcttatt	0.000			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30391355	30391357	+	IGR	DEL	GGA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30391355_30391357delGGA								YPEL5 (7957 upstream) : LBH (63040 downstream)																							atggatggatggatggatggatg	0.064													5	5	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31378449	31378449	+	5'Flank	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31378449delT	uc010ezp.1	-									Q96FL9	GLT14_HUMAN	Homo sapiens GALNT14 mRNA for UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14, complete cds.							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					gtgttaagtcttaccagctaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	31749108	31749108	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31749108delA								XDH (111497 upstream) : SRD5A2 (548 downstream)																							AGGTTGGACTAAATACTATTT	0.398													4	2	---	---	---	---	
TTC27	55622	broad.mit.edu	37	2	32999250	32999251	+	Intron	INS	-	T	T	rs71407471		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32999250_32999251insT	uc002rom.2	+						TTC27_uc010ymx.1_Intron|TTC27_uc002ron.2_Intron	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1						cttccttttacttttttttttt	0.000													4	2	---	---	---	---	
CRIM1	51232	broad.mit.edu	37	2	36747069	36747070	+	Intron	INS	-	AAAA	AAAA	rs142007242	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36747069_36747070insAAAA	uc002rpd.2	+							NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor						nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				AGGTAGAAAATAGAAAAAAGGA	0.337													3	4	---	---	---	---	
EIF2AK2	5610	broad.mit.edu	37	2	37376709	37376710	+	Intron	INS	-	G	G	rs141494566	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37376709_37376710insG	uc010ynh.1	-						EIF2AK2_uc010fab.1_5'Flank|EIF2AK2_uc010yng.1_5'Flank|EIF2AK2_uc010fac.2_Intron|EIF2AK2_uc010fad.2_Intron	NM_002759	NP_002750	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha						evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)				acggttcccatggcacaaattt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37975948	37975948	+	IGR	DEL	T	-	-	rs66540971		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37975948delT								CDC42EP3 (76622 upstream) : FAM82A1 (176514 downstream)																							ACTCATTTGCTGAATTTCTTC	0.423													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41124847	41124848	+	IGR	DEL	AT	-	-	rs143740713		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41124847_41124848delAT								SLC8A1 (385272 upstream) : None (None downstream)																							GGACTCACGCATATATACTACT	0.139													3	5	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42908820	42908820	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42908820delT	uc002rso.1	+						MTA3_uc002rsp.1_Intron|MTA3_uc002rsq.2_Intron|MTA3_uc002rsr.2_Intron	NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						gcccagctaattttttatttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43352023	43352024	+	IGR	DEL	CA	-	-	rs112160221		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43352023_43352024delCA								HAAO (332272 upstream) : ZFP36L2 (97518 downstream)																							CACATGCGCGCACACACACACA	0.559													4	2	---	---	---	---	
PLEKHH2	130271	broad.mit.edu	37	2	43934347	43934348	+	Intron	INS	-	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43934347_43934348insG	uc010yny.1	+						PLEKHH2_uc002rte.3_Intron|PLEKHH2_uc002rtf.3_Intron	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H							cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				aaaaaaaaaaaaaaaaaaaTTC	0.173													14	7	---	---	---	---	
ABCG5	64240	broad.mit.edu	37	2	44064172	44064173	+	Intron	INS	-	CG	CG	rs150590590	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44064172_44064173insCG	uc002rtn.2	-						ABCG5_uc002rto.2_Intron|ABCG5_uc002rtp.2_Intron|ABCG8_uc002rtq.2_5'Flank|ABCG8_uc010yoa.1_5'Flank	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				tgtctcaaaaaagaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	44361351	44361354	+	IGR	DEL	GTTG	-	-	rs149909355		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44361351_44361354delGTTG								LRPPRC (138207 upstream) : PPM1B (34646 downstream)																							gtttttttttgttgtttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45341258	45341265	+	IGR	DEL	ACACACAC	-	-	rs72479063		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45341258_45341265delACACACAC								SIX2 (104715 upstream) : SRBD1 (274555 downstream)																							TTTGGCATGAacacacacacacacacac	0.370													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46223763	46223763	+	Intron	DEL	A	-	-	rs71394866		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46223763delA	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			gtctattgataacaattgatt	0.000													2	4	---	---	---	---	
C2orf61	285051	broad.mit.edu	37	2	47306468	47306470	+	Intron	DEL	CTC	-	-	rs79869043		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47306468_47306470delCTC	uc010fbd.2	-									Q8N801	CB061_HUMAN	Homo sapiens cDNA FLJ40172 fis, clone TESTI2016896.												0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			tctggaagagctcctcctcctct	0.158													4	5	---	---	---	---	
C2orf61	285051	broad.mit.edu	37	2	47307648	47307648	+	Intron	DEL	T	-	-	rs11297773		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47307648delT	uc010fbd.2	-									Q8N801	CB061_HUMAN	Homo sapiens cDNA FLJ40172 fis, clone TESTI2016896.												0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			ttctttcttcttttttttttt	0.035													7	4	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	50380651	50380652	+	Intron	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50380651_50380652delTG	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			tttgttcttttgggttcttctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53068909	53068910	+	IGR	INS	-	GGAGGGAGAA	GGAGGGAGAA	rs143857210	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53068909_53068910insGGAGGGAGAA								None (None upstream) : ASB3 (828208 downstream)																							AAAGAAGAATgggagggagaaa	0.168													4	2	---	---	---	---	
PSME4	23198	broad.mit.edu	37	2	54199743	54199744	+	5'Flank	INS	-	A	A	rs79529921		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54199743_54199744insA	uc002rxp.2	-						PSME4_uc010fbu.1_5'Flank|PSME4_uc010fbv.1_5'Flank	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			gactccgtctcaaaaaaaaaaa	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56204177	56204177	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56204177delA	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																		ttgctgtgccaaaaaaaaaaa	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60580155	60580156	+	IGR	DEL	AC	-	-	rs147505191		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60580155_60580156delAC								None (None upstream) : BCL11A (98147 downstream)																							CATTACAGCAacacacacacac	0.460													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	61106056	61106056	+	Intron	DEL	G	-	-	rs140938600		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61106056delG	uc002sal.1	-						REL_uc002sam.1_5'Flank|REL_uc002san.1_5'Flank					Homo sapiens cDNA FLJ16341 fis, clone TESTI2013381.																		atactactgtggttttttgtt	0.000													4	2	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61525914	61525915	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61525914_61525915insA	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			AATGATGGATTAAAAAAAAAAA	0.342													3	3	---	---	---	---	
EHBP1	23301	broad.mit.edu	37	2	63212721	63212721	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63212721delC	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TGTAGGCTCTCTATAGTTttg	0.219									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	68007808	68007809	+	IGR	INS	-	A	A	rs142219065	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68007808_68007809insA								ETAA1 (370275 upstream) : C1D (261524 downstream)																							gactctgtctcaaaaaaaaaag	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70319291	70319291	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70319291delT								PCBP1 (2959 upstream) : LOC100133985 (31878 downstream)																							TCTCCAAACATTTTCTTAAAG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72103296	72103297	+	IGR	DEL	GT	-	-	rs72120006		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72103296_72103297delGT								DYSF (189404 upstream) : CYP26B1 (253070 downstream)																							GCTGCAGAGGgtgtgtgtgtgt	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72226674	72226674	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72226674delT								DYSF (312782 upstream) : CYP26B1 (129693 downstream)																							gtgtccagtcttaacttactg	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73577805	73577806	+	IGR	DEL	AC	-	-	rs5832101		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73577805_73577806delAC								EGR4 (56976 upstream) : ALMS1 (35080 downstream)																							tgaatgaCGTacacacacacac	0.084													4	2	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77091784	77091784	+	Intron	DEL	C	-	-	rs62173108		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77091784delC	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		gaaactccatcccaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85761637	85761637	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85761637delG								SH2D6 (97487 upstream) : MAT2A (4651 downstream)																							gtcctgccttggggcaggtga	0.000													4	2	---	---	---	---	
USP39	10713	broad.mit.edu	37	2	85876225	85876225	+	3'UTR	DEL	T	-	-	rs67966554		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85876225delT	uc002sqe.2	+	14					USP39_uc002sqb.2_3'UTR|USP39_uc010ysu.1_3'UTR|USP39_uc010ysv.1_3'UTR|USP39_uc002sqf.2_3'UTR|USP39_uc002sqg.2_3'UTR|USP39_uc010fgo.2_3'UTR	NM_006590	NP_006581	Q53GS9	SNUT2_HUMAN	ubiquitin specific protease 39						spliceosome assembly|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1						AACTTATGTCTTGAGTATCTG	0.433											OREG0014749	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1	5	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	86987886	86987886	+	Intron	DEL	A	-	-	rs71377100		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86987886delA	uc010ytm.1	+						RMND5A_uc002srs.3_Intron|RMND5A_uc002srr.2_Intron	NM_022780	NP_073617	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog											ovary(1)|skin(1)	2						gaaagatttgaaaaaggacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88744862	88744862	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88744862delT								THNSL2 (258717 upstream) : FOXI3 (2864 downstream)																							ACCGTTCCCATAAATTTGACA	0.259													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91784574	91784579	+	IGR	DEL	TTAACT	-	-	rs67885824		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91784574_91784579delTTAACT								None (None upstream) : LOC654342 (20613 downstream)																							acttaatacattaactttaaatcccg	0.073													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91917430	91917431	+	IGR	INS	-	AAAA	AAAA			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91917430_91917431insAAAA								LOC654342 (69455 upstream) : GGT8P (45937 downstream)																							atctgaaaaccaaaaaaaaCAc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92324580	92324580	+	IGR	DEL	C	-	-	rs76225255	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92324580delC								FKSG73 (194086 upstream) : None (None downstream)																							ggagcgctttcaggcctatgg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	95669673	95669674	+	IGR	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95669673_95669674delCA								TEKT4 (127105 upstream) : MAL (21805 downstream)																							aatacacatgcacacacacaca	0.000													4	2	---	---	---	---	
TRIM43	129868	broad.mit.edu	37	2	96265407	96265408	+	3'UTR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96265407_96265408insT	uc002suv.2	+	7						NM_138800	NP_620155	Q96BQ3	TRI43_HUMAN	tripartite motif-containing 43							intracellular	zinc ion binding			ovary(1)	1						ACTGTTCAGGCTTTTTTGTACT	0.307													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102228662	102228662	+	IGR	DEL	A	-	-	rs67794394		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102228662delA								RFX8 (137497 upstream) : MAP4K4 (85826 downstream)																							TGAGGCAAAGAAAAAAAAAAA	0.259													4	2	---	---	---	---	
NCK2	8440	broad.mit.edu	37	2	106382447	106382448	+	Intron	INS	-	A	A	rs139668427	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106382447_106382448insA	uc002tdg.2	+						NCK2_uc002tdh.2_Intron	NM_003581	NP_003572	O43639	NCK2_HUMAN	NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2						aGGTGACGCTTACACTGCACAG	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107932138	107932139	+	IGR	INS	-	GT	GT	rs147987530	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107932138_107932139insGT								ST6GAL2 (428575 upstream) : LOC729121 (507381 downstream)																							tgtaggtgtgagtgtgtgtgtg	0.000													2	4	---	---	---	---	
EDAR	10913	broad.mit.edu	37	2	109597437	109597438	+	Intron	INS	-	G	G	rs147475923	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109597437_109597438insG	uc002teq.3	-						EDAR_uc010fjn.2_Intron|EDAR_uc010yws.1_Intron	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor						apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						GACTAGACCGTGGGAATGACTG	0.441													3	3	---	---	---	---	
ACOXL	55289	broad.mit.edu	37	2	111815554	111815555	+	Intron	INS	-	AG	AG	rs72531615		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111815554_111815555insAG	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						GAGTCTAGCACGGCTTGCGGGT	0.545													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	117952084	117952087	+	IGR	DEL	TTTT	-	-	rs141070349		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117952084_117952087delTTTT								None (None upstream) : DDX18 (620168 downstream)																							gttgttgttgttttgttgtcgatg	0.034													3	4	---	---	---	---	
INSIG2	51141	broad.mit.edu	37	2	118851625	118851626	+	Intron	INS	-	GAA	GAA			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118851625_118851626insGAA	uc002tlk.2	+						INSIG2_uc010yye.1_Intron	NM_016133	NP_057217	Q9Y5U4	INSI2_HUMAN	insulin induced protein 2						ER-nuclear sterol response pathway	SREBP-SCAP-Insig complex				ovary(1)|central_nervous_system(1)	2						atgatgatgatgGAGAGTTCTG	0.238													4	2	---	---	---	---	
SCTR	6344	broad.mit.edu	37	2	120284754	120284755	+	5'Flank	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120284754_120284755delAC	uc002tma.2	-							NM_002980	NP_002971	P47872	SCTR_HUMAN	secretin receptor precursor						digestion|excretion	integral to plasma membrane	secretin receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3					Secretin(DB00021)	tgtctgaaagacacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120761486	120761488	+	IGR	DEL	TGT	-	-	rs147667346	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120761486_120761488delTGT								PTPN4 (26449 upstream) : EPB41L5 (9181 downstream)																							gctttggttgtgttgttgttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122611101	122611102	+	IGR	DEL	TT	-	-	rs145502112		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122611101_122611102delTT								TSN (85675 upstream) : None (None downstream)																							tctctctctctttctttctttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123986970	123986970	+	IGR	DEL	T	-	-	rs145800113		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123986970delT								None (None upstream) : CNTNAP5 (795894 downstream)																							ttgcatggagttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129185429	129185430	+	IGR	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129185429_129185430delGT								HS6ST1 (109258 upstream) : None (None downstream)																							gtgcatgttcgtgtgtgtgtgt	0.163													4	2	---	---	---	---	
FAM128B	80097	broad.mit.edu	37	2	130945640	130945640	+	Intron	DEL	A	-	-	rs35336011		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130945640delA	uc002tqu.2	+							NM_025029	NP_079305	Q6NZ67	MZT2B_HUMAN	hypothetical protein LOC80097							centrosome|gamma-tubulin ring complex|spindle	protein binding				0	Colorectal(110;0.1)					CCCACCACTCAAAAAAAAAAA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132779445	132779445	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132779445delC								C2orf27B (220211 upstream) : NCRNA00164 (125719 downstream)																							ACTTCATACTCCCATTTGATA	0.403													4	4	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	133009045	133009045	+	Intron	DEL	C	-	-	rs113324698		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133009045delC	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						gacacgttttcctccacccct	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133035190	133035193	+	IGR	DEL	GAAG	-	-	rs139877197		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133035190_133035193delGAAG								NCRNA00164 (19648 upstream) : GPR39 (138954 downstream)																							ATAAATgaaagaaggaaggaagga	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133036945	133036945	+	IGR	DEL	C	-	-	rs76972194	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133036945delC								NCRNA00164 (21403 upstream) : GPR39 (137202 downstream)																							cgagcttttgcccttctgctc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133064260	133064261	+	Intron	INS	-	C	C	rs148351345	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133064260_133064261insC	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		taatggcacctcctgtcacttc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133106660	133106661	+	IGR	INS	-	T	T	rs150309648	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133106660_133106661insT								NCRNA00164 (91118 upstream) : GPR39 (67486 downstream)																							CTCCATGCCCCTTTTTTTTGGT	0.317													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133117293	133117294	+	IGR	INS	-	A	A	rs149418880	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133117293_133117294insA								NCRNA00164 (101751 upstream) : GPR39 (56853 downstream)																							aatcaacaagcagcagcaagta	0.000													4	4	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133595046	133595046	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133595046delT	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						cttccagcccttctactgcgt	0.000													4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142268480	142268481	+	Intron	INS	-	CA	CA	rs140983947	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142268480_142268481insCA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		cacacacaccccacacaaacat	0.178										TSP Lung(27;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	143291973	143291973	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143291973delA								LRP1B (402703 upstream) : KYNU (343222 downstream)																							TGAAAAAATGAAAAAAAAAGG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147993360	147993361	+	IGR	DEL	AC	-	-	rs10678843		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147993360_147993361delAC								PABPC1P2 (644803 upstream) : ACVR2A (608725 downstream)																							AACACGacatacacacacacac	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151543191	151543191	+	IGR	DEL	A	-	-	rs79543469		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151543191delA								RND3 (199011 upstream) : RBM43 (561538 downstream)																							aatccaggagaaaaaaaaaaa	0.124													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	155967234	155967234	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155967234delT								KCNJ3 (254220 upstream) : None (None downstream)																							tcaccctaccttttggtacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157798215	157798216	+	IGR	INS	-	ACAC	ACAC	rs149850281	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157798215_157798216insACAC								GPD2 (327968 upstream) : GALNT5 (316124 downstream)																							GAAATAGATAAacacacacaca	0.193													2	4	---	---	---	---	
CSRNP3	80034	broad.mit.edu	37	2	166377684	166377684	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166377684delA	uc002udf.2	+							NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5						TGGGAAAGCCAAAAAAAAAAA	0.383													4	2	---	---	---	---	
METTL8	79828	broad.mit.edu	37	2	172198066	172198066	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172198066delT	uc010zdo.1	-						METTL8_uc002ugu.3_Intron|METTL8_uc002ugv.3_Intron|METTL8_uc002ugt.3_Intron|METTL8_uc002ugs.3_Intron|METTL8_uc010zdp.1_Intron	NM_024770	NP_079046	B3KW44	B3KW44_HUMAN	methyltransferase like 8								methyltransferase activity			ovary(1)	1						TTTTTTTCCCTTTTTTTTTTT	0.219													4	2	---	---	---	---	
SCRN3	79634	broad.mit.edu	37	2	175277228	175277228	+	Intron	DEL	T	-	-	rs67941361		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175277228delT	uc002uiq.2	+						SCRN3_uc010zen.1_Intron|SCRN3_uc010zeo.1_Intron|SCRN3_uc002uis.2_Intron	NM_024583	NP_078859	Q0VDG4	SCRN3_HUMAN	secernin 3						proteolysis		dipeptidase activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.229)			ttctctcccatctagaggaat	0.000													0	6	---	---	---	---	
OSBPL6	114880	broad.mit.edu	37	2	179146989	179146990	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179146989_179146990delAC	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron|OSBPL6_uc002ulz.2_5'Flank	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			GTAGCCAAGGACACACACACAC	0.366													4	2	---	---	---	---	
CWC22	57703	broad.mit.edu	37	2	180823272	180823273	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180823272_180823273insT	uc010frh.1	-						CWC22_uc002uno.2_Intron|CWC22_uc002unp.2_Intron	NM_020943	NP_065994	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein homolog							catalytic step 2 spliceosome	protein binding|RNA binding				0						aaaacattatgttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	190284645	190284645	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190284645delA								COL5A2 (240040 upstream) : WDR75 (21514 downstream)																							ggaggagaagaaggagagggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	199882503	199882503	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199882503delA								PLCL1 (867897 upstream) : SATB2 (251721 downstream)																							gagcagaaggaaagccagcat	0.000													4	2	---	---	---	---	
SPATS2L	26010	broad.mit.edu	37	2	201284434	201284434	+	Intron	DEL	T	-	-	rs149944431		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201284434delT	uc002uvn.3	+						SPATS2L_uc010fst.2_Intron|SPATS2L_uc002uvo.3_Intron|SPATS2L_uc002uvp.3_Intron|SPATS2L_uc002uvq.3_Intron|SPATS2L_uc002uvr.3_Intron|SPATS2L_uc010zhc.1_Intron	NM_015535	NP_056350	Q9NUQ6	SPS2L_HUMAN	SPATS2-like protein isoform a							cytoplasm|nucleolus				ovary(2)|pancreas(1)	3						AGTCAGAGGAttttttttttt	0.244													4	2	---	---	---	---	
SPATS2L	26010	broad.mit.edu	37	2	201294156	201294156	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201294156delA	uc002uvn.3	+						SPATS2L_uc010fst.2_Intron|SPATS2L_uc002uvo.3_Intron|SPATS2L_uc002uvp.3_Intron|SPATS2L_uc002uvq.3_Intron|SPATS2L_uc002uvr.3_Intron|SPATS2L_uc010zhc.1_Intron	NM_015535	NP_056350	Q9NUQ6	SPS2L_HUMAN	SPATS2-like protein isoform a							cytoplasm|nucleolus				ovary(2)|pancreas(1)	3						ctgatcgaagaaggtgtgTGG	0.244													4	2	---	---	---	---	
PLEKHM3	389072	broad.mit.edu	37	2	208757850	208757850	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208757850delA	uc002vcl.2	-							NM_001080475	NP_001073944	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1						GTTGGAAAACAAAAAAAGCGT	0.403													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	208921915	208921915	+	IGR	DEL	T	-	-	rs74577733	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208921915delT								PLEKHM3 (31631 upstream) : CRYGD (64417 downstream)																							CAAGGTGGTGTTTTTTTTTTT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210011135	210011135	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210011135delA								PTH2R (306317 upstream) : MAP2 (277636 downstream)																							gtaaaaggggaaaaggcttta	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217758385	217758385	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217758385delC								TNP1 (33603 upstream) : DIRC3 (390363 downstream)																							atcacaagggcccttaagagt	0.000													4	2	---	---	---	---	
DIRC3	729582	broad.mit.edu	37	2	218582889	218582894	+	Intron	DEL	ACACAC	-	-	rs66749630		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218582889_218582894delACACAC	uc002vgo.2	-							NR_026597				Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0						acacacacaaacacacacacacacac	0.209													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	218656500	218656500	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218656500delT								DIRC3 (35184 upstream) : TNS1 (8012 downstream)																							cgccctctccttcctcttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	218657788	218657789	+	IGR	INS	-	AG	AG	rs149710914	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218657788_218657789insAG								DIRC3 (36472 upstream) : TNS1 (6723 downstream)																							gatgtggaaacaagcacagcag	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220857025	220857025	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220857025delG								SLC4A3 (350324 upstream) : None (None downstream)																							TTTCTGGCTAGGCCCTGGGCT	0.453													4	2	---	---	---	---	
KIAA1486	57624	broad.mit.edu	37	2	226336693	226336693	+	Intron	DEL	T	-	-	rs11307176		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226336693delT	uc002voe.2	+						KIAA1486_uc010fxa.1_Intron	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		tgagtacttattatattccct	0.114													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	226935015	226935016	+	IGR	DEL	CT	-	-	rs113028299		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226935015_226935016delCT								KIAA1486 (339544 upstream) : IRS1 (661018 downstream)																							gtgacacttcctctctctctct	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	227124150	227124150	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227124150delT								KIAA1486 (528679 upstream) : IRS1 (471884 downstream)																							tgttccctggtttcctgtggg	0.214													4	2	---	---	---	---	
IRS1	3667	broad.mit.edu	37	2	227609102	227609102	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227609102delA	uc002voh.3	-							NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1						fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TCTGATCCTTAAACAGGCCTA	0.413													4	2	---	---	---	---	
MFF	56947	broad.mit.edu	37	2	228220704	228220706	+	Intron	DEL	AAA	-	-	rs59843055		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228220704_228220706delAAA	uc002vos.2	+						MFF_uc002vot.2_Intron|MFF_uc002vou.2_Intron|MFF_uc002vov.2_Intron|MFF_uc002vow.2_Intron|MFF_uc002vox.2_Intron|MFF_uc002voy.2_Intron|MFF_uc002voz.2_Intron|MFF_uc002vpa.2_Intron	NM_020194	NP_064579	Q9GZY8	MFF_HUMAN	mitochondrial fission factor							integral to membrane|mitochondrial outer membrane				large_intestine(1)	1						GGCCAGTAACAAAGAATCTTTAG	0.315													4	2	---	---	---	---	
PID1	55022	broad.mit.edu	37	2	230043565	230043565	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230043565delG	uc002vpr.3	-						PID1_uc002vps.3_Intron|PID1_uc002vpt.3_Intron|PID1_uc002vpu.3_Intron	NM_001100818	NP_001094288	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1							cytoplasm				breast(3)|skin(1)	4		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		AGAAGGAAGTGGGACCGTCCC	0.522													4	2	---	---	---	---	
DGKD	8527	broad.mit.edu	37	2	234359852	234359852	+	Intron	DEL	T	-	-	rs3214825		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234359852delT	uc002vui.1	+						DGKD_uc002vuj.1_Intron|DGKD_uc010fyh.1_Intron|DGKD_uc010fyi.1_Intron	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TGAAAAGTGCTTTTTTTTTTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238860092	238860095	+	IGR	DEL	GGAG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238860092_238860095delGGAG								RAMP1 (39339 upstream) : UBE2F (15605 downstream)																							aaagaaGGAAGGAGGGAGGGAGGG	0.088													5	3	---	---	---	---	
FARP2	9855	broad.mit.edu	37	2	242352633	242352634	+	Intron	INS	-	T	T	rs141753202	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242352633_242352634insT	uc002wbi.1	+						FARP2_uc010zoq.1_Intron|FARP2_uc010zor.1_Intron	NM_014808	NP_055623	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2						axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		ATTTGGGATAATTTTTTTTTAC	0.248													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	1877419	1877419	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1877419delT								CNTN6 (432142 upstream) : CNTN4 (263131 downstream)																							CATTTCAGGGTTTTTTTTTTT	0.318													4	2	---	---	---	---	
IQSEC1	9922	broad.mit.edu	37	3	12960608	12960609	+	Intron	INS	-	C	C	rs140960248	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12960608_12960609insC	uc003bxt.2	-						IQSEC1_uc003bxu.3_Intron|IQSEC1_uc011auw.1_Intron	NM_014869	NP_055684	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1 isoform b						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1						TGTAGAGGAGGCCCGGCCTCCT	0.609													4	2	---	---	---	---	
C3orf19	51244	broad.mit.edu	37	3	14706745	14706746	+	Intron	INS	-	ATTG	ATTG	rs142447115	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14706745_14706746insATTG	uc003byw.2	+						C3orf19_uc010hei.1_Intron|C3orf19_uc010hej.2_Intron	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244												0						AGTAAGGAGATattgattgatt	0.386													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14855245	14855246	+	IGR	INS	-	AG	AG	rs151173653	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14855245_14855246insAG								C3orf20 (40705 upstream) : FGD5 (5223 downstream)																							ccagttaaggcagagccaggtg	0.094													3	4	---	---	---	---	
KCNH8	131096	broad.mit.edu	37	3	19453269	19453270	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19453269_19453270delAC	uc003cbk.1	+						KCNH8_uc011awe.1_Intron|KCNH8_uc010hex.1_Intron|KCNH8_uc011awf.1_Intron	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						acacacacagacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	19840020	19840035	+	IGR	DEL	AGGAAGGCAGGAAGGG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19840020_19840035delAGGAAGGCAGGAAGGG								KCNH8 (262885 upstream) : EFHB (80933 downstream)																							gaagggagaaaggaaggcaggaagggaggaaggcag	0.005													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	24718765	24718766	+	IGR	INS	-	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24718765_24718766insG								THRB (182312 upstream) : RARB (497057 downstream)																							tattatacaatgggggcaggga	0.000													4	2	---	---	---	---	
NEK10	152110	broad.mit.edu	37	3	27255134	27255134	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27255134delC	uc010hfk.2	-						NEK10_uc003cds.1_Intron|NEK10_uc010hfj.2_Intron			Q6ZWH5	NEK10_HUMAN	RecName: Full=Serine/threonine-protein kinase Nek10;          EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10;								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						aaacatgcctcattataatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	42390290	42390291	+	IGR	DEL	TG	-	-	rs72178040		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42390290_42390291delTG								CCK (82628 upstream) : LYZL4 (48286 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	45424177	45424177	+	IGR	DEL	T	-	-	rs113551900		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45424177delT								TMEM158 (156363 upstream) : LARS2 (5898 downstream)																							ttttcttttcttttttttttg	0.025													4	2	---	---	---	---	
ZNF589	51385	broad.mit.edu	37	3	48292887	48292887	+	Intron	DEL	A	-	-	rs113298003		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48292887delA	uc003csl.3	+						ZNF589_uc010hjt.1_Intron|ZNF589_uc003csn.2_Intron|ZNF589_uc011bbg.1_Intron|ZNF589_uc003csm.2_Intron	NM_016089	NP_057173	Q86UQ0	ZN589_HUMAN	zinc finger protein 589						regulation of transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		actccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BSN	8927	broad.mit.edu	37	3	49708575	49708578	+	3'UTR	DEL	GTGC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49708575_49708578delGTGC	uc003cxe.3	+	12					APEH_uc010hkw.1_5'Flank|APEH_uc003cxf.2_5'Flank	NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein						synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		Atgtgtgtatgtgcgtgcgtgcgt	0.422													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75737316	75737316	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75737316delA								MIR1324 (57307 upstream) : ZNF717 (21478 downstream)																							gtagtcacttaaaaaatgttt	0.159													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75865423	75865424	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75865423_75865424insT								ZNF717 (30753 upstream) : None (None downstream)																							CTTTTTTCATGTTTTTTTAAAA	0.342													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	99070662	99070663	+	IGR	INS	-	T	T	rs35423469		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99070662_99070663insT								DCBLD2 (450129 upstream) : COL8A1 (286791 downstream)																							ATATTTTTCTGTTTTTTTTTTT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	99166423	99166424	+	IGR	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99166423_99166424delAC								DCBLD2 (545890 upstream) : COL8A1 (191030 downstream)																							catctcaaaaacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	100781708	100781709	+	IGR	INS	-	T	T	rs138630967	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100781708_100781709insT								ABI3BP (69374 upstream) : IMPG2 (163579 downstream)																							ctatccactgattttttttttc	0.158													1	7	---	---	---	---	
ZPLD1	131368	broad.mit.edu	37	3	102141659	102141660	+	Intron	INS	-	TTG	TTG	rs148309697	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102141659_102141660insTTG	uc003dvs.1	+							NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1							integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5						ATAGGAACTTTTTGTTGTTGTT	0.396													3	3	---	---	---	---	
PHLDB2	90102	broad.mit.edu	37	3	111574358	111574359	+	Intron	INS	-	CTTT	CTTT	rs143529595	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111574358_111574359insCTTT	uc003dyc.2	+							NM_001134437	NP_001127909	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						tcttttctttcctttctttctt	0.109													2	5	---	---	---	---	
SIDT1	54847	broad.mit.edu	37	3	113272475	113272477	+	Intron	DEL	ATC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113272475_113272477delATC	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						GAAAAAAGAAATCATGCACAGAA	0.443													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	119410266	119410267	+	IGR	INS	-	A	A	rs34077281		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119410266_119410267insA								COX17 (14023 upstream) : C3orf15 (11602 downstream)																							atgagacccagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	119994949	119994950	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119994949_119994950insT								GPR156 (31624 upstream) : LRRC58 (48626 downstream)																							gatgctccggctttgttttttt	0.168													4	2	---	---	---	---	
SEMA5B	54437	broad.mit.edu	37	3	122726566	122726566	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122726566delA	uc003efz.1	-						SEMA5B_uc011bju.1_Intron|SEMA5B_uc003ega.1_Intron|SEMA5B_uc010hro.1_Intron|SEMA5B_uc010hrp.1_Intron	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1						cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)		tcccaacagcaaaaaggccct	0.000													4	2	---	---	---	---	
ADCY5	111	broad.mit.edu	37	3	123104141	123104142	+	Intron	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123104141_123104142delCA	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		Gacacacacgcacacacacaca	0.465													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124315917	124315920	+	Intron	DEL	ACAA	-	-	rs140782289		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124315917_124315920delACAA	uc003ehg.2	+						KALRN_uc003ehi.2_Intron|KALRN_uc003ehk.2_Intron|KALRN_uc003ehj.2_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						aaacaaaaacacaaacaaaacaaa	0.157													4	2	---	---	---	---	
ITGB5	3693	broad.mit.edu	37	3	124486035	124486035	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124486035delG	uc003eho.2	-						ITGB5_uc010hrx.2_Intron	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)		AATGGGTCCTGGGGAGGAACA	0.512													4	2	---	---	---	---	
ZNF148	7707	broad.mit.edu	37	3	125058372	125058372	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125058372delC	uc003ehx.3	-						ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799	Q9UQR1	ZN148_HUMAN	zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4						TGCATCTATTCCCTAGCAACC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	125502724	125502724	+	IGR	DEL	C	-	-	rs60485712		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125502724delC								OSBPL11 (188343 upstream) : MIR548I1 (6523 downstream)																							CAAAAGCTCGCAGGTGATTCT	0.502													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126836256	126836257	+	IGR	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126836256_126836257delTG								PLXNA1 (80028 upstream) : TPRA1 (455651 downstream)																							GAGTTATTTTtgtgtgtgtgtg	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126885598	126885598	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126885598delT								PLXNA1 (129370 upstream) : TPRA1 (406310 downstream)																							ccacgtggcctgagctgcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127150167	127150168	+	IGR	INS	-	TGTG	TGTG	rs147999726	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127150167_127150168insTGTG								PLXNA1 (393939 upstream) : TPRA1 (141740 downstream)																							gcgcgtgtgcttgtgtgtgtgt	0.366													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127169929	127169932	+	IGR	DEL	TGTG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127169929_127169932delTGTG								PLXNA1 (413701 upstream) : TPRA1 (121976 downstream)																							AGGGACAGCAtgtgtgtgtgtgtg	0.397													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129075128	129075128	+	IGR	DEL	T	-	-	rs11292747		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129075128delT								C3orf47 (31716 upstream) : RPL32P3 (26550 downstream)																							ttcttttttctttttttttga	0.219													3	6	---	---	---	---	
MRPL3	11222	broad.mit.edu	37	3	131196736	131196737	+	Intron	INS	-	TCC	TCC			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131196736_131196737insTCC	uc003eoh.2	-						MRPL3_uc011blo.1_Intron|MRPL3_uc011blp.1_Intron	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3						translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						TTGTCATCATTTCCTCCCTATT	0.366													4	2	---	---	---	---	
NCRNA00119	348808	broad.mit.edu	37	3	132509151	132509152	+	Intron	INS	-	GTT	GTT	rs144145674	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132509151_132509152insGTT	uc003epg.1	+							NR_002811				Homo sapiens cDNA clone IMAGE:4826885.												0						aaacaagggcagttgtacccat	0.000													2	7	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134891878	134891878	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134891878delT	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						AAATAGtttcttttttttttt	0.224													4	2	---	---	---	---	
TMEM22	80723	broad.mit.edu	37	3	136550731	136550732	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136550731_136550732insT	uc003erf.3	+						TMEM22_uc003erg.3_Intron|TMEM22_uc010hub.2_Intron	NM_001097600	NP_001091069	Q8TBE7	TMM22_HUMAN	transmembrane protein 22							Golgi apparatus|integral to membrane				ovary(1)	1						tGAGTCTAGTCTTTTTTTTTTT	0.173													4	2	---	---	---	---	
C3orf72	401089	broad.mit.edu	37	3	138671355	138671355	+	3'UTR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138671355delT	uc003esx.1	+	3						NM_001040061	NP_001035150	Q6ZUU3	CC072_HUMAN	chromosome 3 open reading frame 72												0						TATGAAACACttttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139030954	139030955	+	IGR	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139030954_139030955delTG								PISRT1 (78590 upstream) : MRPS22 (31843 downstream)																							ATtgtgtgcctgtgtgtgtgtg	0.396													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139636319	139636320	+	IGR	INS	-	A	A	rs139960545	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139636319_139636320insA								NMNAT3 (239479 upstream) : CLSTN2 (17707 downstream)																							TTCTTATGTTTACATCCCCTTG	0.515													2	6	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140013407	140013407	+	Intron	DEL	T	-	-	rs11304144		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140013407delT	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						CCCCAATGTCTTTTTTTTTTT	0.249										HNSCC(16;0.037)			4	2	---	---	---	---	
ZBTB38	253461	broad.mit.edu	37	3	141146721	141146721	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141146721delG	uc003etw.2	+						ZBTB38_uc010hun.2_Intron|ZBTB38_uc010huo.2_Intron|ZBTB38_uc003ety.2_Intron|ZBTB38_uc010hup.2_Intron	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						ATCTTCCTGAGGCATTTACTT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141384384	141384387	+	IGR	DEL	AAGG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141384384_141384387delAAGG								RASA2 (53187 upstream) : RNF7 (72664 downstream)																							aggagggggcaaggaaggaaggaa	0.000													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141873536	141873537	+	IGR	INS	-	A	A	rs147206306	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141873536_141873537insA								TFDP2 (5225 upstream) : GK5 (2832 downstream)																							actatccatggacactaaaact	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	142834080	142834081	+	IGR	DEL	AG	-	-	rs77135430		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142834080_142834081delAG								SR140 (54513 upstream) : CHST2 (4587 downstream)																							Atccccactcagggcttctgca	0.213													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145292114	145292114	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145292114delA								None (None upstream) : PLOD2 (495114 downstream)																							aggacagctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145482184	145482185	+	IGR	DEL	AA	-	-	rs72100430		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145482184_145482185delAA								None (None upstream) : PLOD2 (305043 downstream)																							agagacagacaaagagagagag	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145730021	145730022	+	IGR	INS	-	TTG	TTG	rs139209223	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145730021_145730022insTTG								None (None upstream) : PLOD2 (57206 downstream)																							CTTTTCTATTTttgttgttgtt	0.163													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147175032	147175033	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147175032_147175033insT								ZIC1 (40528 upstream) : None (None downstream)																							AAGAGAAAGCCttttttttttt	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151188534	151188535	+	IGR	INS	-	AGCAGC	AGCAGC	rs149380286	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151188534_151188535insAGCAGC								IGSF10 (12037 upstream) : AADACL2 (263169 downstream)																							aattgactaaaagcagcagcag	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152233144	152233147	+	IGR	DEL	CGTG	-	-	rs10670854		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152233144_152233147delCGTG								MBNL1 (49576 upstream) : P2RY1 (319589 downstream)																							Tacacacacacgtgcacacgcgca	0.196													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152495269	152495271	+	IGR	DEL	TTC	-	-	rs10576161		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152495269_152495271delTTC								MBNL1 (311701 upstream) : P2RY1 (57465 downstream)																							GCTGCTGCTTTTCTTGTTTCTCC	0.345													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152876634	152876634	+	IGR	DEL	A	-	-	rs68019000		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152876634delA								P2RY1 (320793 upstream) : RAP2B (3395 downstream)																							acactgtctcaaaaaaaaaaa	0.124													4	4	---	---	---	---	
SGEF	26084	broad.mit.edu	37	3	153933186	153933187	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153933186_153933187insT	uc011bog.1	+						SGEF_uc011boh.1_Intron	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			tcagtctgtgattttttttttt	0.000													4	2	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155244279	155244280	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155244279_155244280delAC	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			tctctctcatacacacacacac	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155767645	155767645	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155767645delC								GMPS (112127 upstream) : KCNAB1 (70692 downstream)																							cctgtagcttccagtgggttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	156473011	156473011	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156473011delA	uc003fax.1	-											Homo sapiens cDNA FLJ31839 fis, clone NT2RP7000086.																		atcaatggacaaggcaccgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157671306	157671307	+	IGR	INS	-	A	A	rs35538130		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157671306_157671307insA								C3orf55 (352287 upstream) : SHOX2 (142494 downstream)																							ggcattgtgacAAAAAAAAAAA	0.149													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157810498	157810498	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157810498delA								C3orf55 (491479 upstream) : SHOX2 (3303 downstream)																							ACTGACATGTAAAATACCCAA	0.358													4	2	---	---	---	---	
MLF1	4291	broad.mit.edu	37	3	158300326	158300327	+	Intron	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158300326_158300327delGT	uc003fcb.2	+						MLF1_uc003fbz.2_Intron|MLF1_uc003fca.2_Intron|MLF1_uc003fbx.2_Intron|MLF1_uc003fcc.2_Intron|MLF1_uc003fby.2_Intron|MLF1_uc010hvx.2_Intron	NM_022443	NP_071888	P58340	MLF1_HUMAN	myeloid leukemia factor 1 isoform 1						cell cycle arrest|myeloid progenitor cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein domain specific binding				0		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			ttaaacctaggtgtgtcgtatt	0.000			T	NPM1	AML								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	158598966	158598967	+	IGR	INS	-	T	T	rs146203714		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158598966_158598967insT								MFSD1 (51462 upstream) : SCHIP1 (188150 downstream)																							atgacaaTAGAttttttttttt	0.054													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159854458	159854458	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159854458delA	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		CTTCGAGGGTAAAAAGGGGGC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162159734	162159734	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162159734delC								OTOL1 (938006 upstream) : None (None downstream)																							gaaagaatgtccagtaatgta	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162464750	162464751	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162464750_162464751insT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																		aataggattacttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163271057	163271058	+	IGR	INS	-	A	A	rs71630474		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163271057_163271058insA								None (None upstream) : MIR1263 (618201 downstream)																							gattcagtctcaaaaaaaaaaa	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163587407	163587409	+	IGR	DEL	AAC	-	-	rs145383905		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163587407_163587409delAAC								None (None upstream) : MIR1263 (301850 downstream)																							GGGAATTGAAAACAACAACAACA	0.414													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165286722	165286722	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165286722delA								SLITRK3 (372253 upstream) : BCHE (203972 downstream)																							CAACAACAACAAAAAAAAAAA	0.060													4	2	---	---	---	---	
PHC3	80012	broad.mit.edu	37	3	169865147	169865148	+	Intron	INS	-	A	A	rs150293279	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169865147_169865148insA	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron|PHC3_uc003fgm.2_Intron|PHC3_uc003fgo.1_3'UTR	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			ATTAGAAAATTAAACGACCAAT	0.252													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	170041525	170041525	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170041525delA								PRKCI (17755 upstream) : SKIL (33948 downstream)																							GAAAAAAAGGAAAAAAAAAAA	0.259													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170323906	170323906	+	Intron	DEL	T	-	-	rs33963145		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170323906delT	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			Cttcttcttcttttttttttt	0.025													4	2	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170818503	170818504	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170818503_170818504insA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhg.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			ACTCCAATAAGAAAAAAAAAAA	0.366													4	2	---	---	---	---	
YEATS2	55689	broad.mit.edu	37	3	183447465	183447465	+	Intron	DEL	T	-	-	rs10708141		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183447465delT	uc003fly.2	+							NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GTTCTTTACAttttttttttt	0.139													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184323647	184323648	+	IGR	INS	-	A	A	rs149083491		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184323647_184323648insA								EPHB3 (23452 upstream) : MAGEF1 (104508 downstream)																							gactacatctcaaaaaaaaaaa	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184393075	184393077	+	IGR	DEL	TCT	-	-	rs148889951	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184393075_184393077delTCT								EPHB3 (92880 upstream) : MAGEF1 (35079 downstream)																							tctatctctctcttttttttttt	0.108													3	3	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184651315	184651316	+	Intron	INS	-	TG	TG	rs144754366	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184651315_184651316insTG	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			ctttcgatctttgtgtgtgtgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184978426	184978427	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184978426_184978427insT								EHHADH (6589 upstream) : MAP3K13 (22327 downstream)																							tttgttttttgttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	185292728	185292728	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185292728delA								LIPH (22359 upstream) : SENP2 (7779 downstream)																							tctgtatcatacccctgccat	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186173679	186173680	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186173679_186173680delAC	uc003fqd.1	-											Homo sapiens cDNA FLJ32735 fis, clone TESTI2001229.																		CACCCCAAAGacacacacacac	0.243													5	3	---	---	---	---	
ADIPOQ	9370	broad.mit.edu	37	3	186557999	186558000	+	5'Flank	INS	-	T	T	rs113407644		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186557999_186558000insT	uc003fra.2	+						ADIPOQ_uc010hyy.2_5'Flank	NM_004797	NP_004788	Q15848	ADIPO_HUMAN	adiponectin precursor						brown fat cell differentiation|cellular response to drug|cellular response to insulin stimulus|detection of oxidative stress|fatty acid beta-oxidation|generation of precursor metabolites and energy|glucose homeostasis|glucose metabolic process|low-density lipoprotein particle clearance|negative regulation of blood pressure|negative regulation of DNA biosynthetic process|negative regulation of ERK1 and ERK2 cascade|negative regulation of eukaryotic cell surface binding|negative regulation of fat cell differentiation|negative regulation of gluconeogenesis|negative regulation of granulocyte differentiation|negative regulation of heterotypic cell-cell adhesion|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of intracellular protein transport|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|negative regulation of macrophage differentiation|negative regulation of MAP kinase activity|negative regulation of phagocytosis|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein autophosphorylation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|negative regulation of synaptic transmission|negative regulation of transcription, DNA-dependent|negative regulation of tumor necrosis factor production|negative regulation of tumor necrosis factor-mediated signaling pathway|positive regulation of cAMP-dependent protein kinase activity|positive regulation of cholesterol efflux|positive regulation of fatty acid metabolic process|positive regulation of glucose import|positive regulation of glycogen (starch) synthase activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of metanephric glomerular visceral epithelial cell development|positive regulation of monocyte chemotactic protein-1 production|positive regulation of myeloid cell apoptosis|positive regulation of protein kinase A signaling cascade|positive regulation of renal albumin absorption|protein homooligomerization|protein localization in plasma membrane|response to glucose stimulus|response to tumor necrosis factor	collagen|endoplasmic reticulum|extracellular space	cytokine activity|eukaryotic cell surface binding|hormone activity|protein homodimerization activity			ovary(1)	1	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		GAAGAAAATACttttttttttt	0.198													4	2	---	---	---	---	
ST6GAL1	6480	broad.mit.edu	37	3	186708439	186708439	+	Intron	DEL	T	-	-	rs111805405		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186708439delT	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron	NM_173216	NP_775323	P15907	SIAT1_HUMAN	ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		CAGGATGTTCTTTTTTTTTTT	0.318													4	3	---	---	---	---	
BCL6	604	broad.mit.edu	37	3	187462599	187462599	+	Intron	DEL	A	-	-	rs3832246		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187462599delA	uc003frq.1	-							NM_001706	NP_001697	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1						negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		ggagcgacggagcaaggaaag	0.294			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187586865	187586865	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187586865delA								BCL6 (123390 upstream) : LPP (284854 downstream)																							aaggcatgataaaaaAAAAAC	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194248674	194248676	+	IGR	DEL	TTC	-	-	rs63445161		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194248674_194248676delTTC								ATP13A3 (59706 upstream) : TMEM44 (59727 downstream)																							ttttctttctttcttctgttctt	0.118													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194559741	194559742	+	IGR	DEL	TG	-	-	rs112371069		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194559741_194559742delTG								FAM43A (149977 upstream) : C3orf21 (229273 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.351													4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195494810	195494812	+	Intron	DEL	ACC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195494810_195494812delACC	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		caccgccactaccaccaccacca	0.227													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195878158	195878159	+	Intron	INS	-	A	A	rs76880138		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195878158_195878159insA	uc011bts.1	+						uc011btt.1_Intron					Homo sapiens cDNA FLJ25996 fis, clone DMC06615.																		gactctgtcacaaaaaaaaaaa	0.173													4	2	---	---	---	---	
SENP5	205564	broad.mit.edu	37	3	196640439	196640440	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196640439_196640440insA	uc003fwz.3	+						SENP5_uc011bty.1_Intron	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5						cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		gactccatctcaaaaaaaaaaa	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197061780	197061782	+	IGR	DEL	TTT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197061780_197061782delTTT								DLG1 (35637 upstream) : BDH1 (174873 downstream)																							TTCCtttttcttttttttttttt	0.207													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197153485	197153487	+	IGR	DEL	TTT	-	-	rs71623351		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197153485_197153487delTTT								DLG1 (127342 upstream) : BDH1 (83168 downstream)																							tctttttttcttttttttttttt	0.182													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197186388	197186389	+	IGR	INS	-	G	G	rs149540272		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197186388_197186389insG								DLG1 (160245 upstream) : BDH1 (50266 downstream)																							tgtggtcgggagggatgCAGTT	0.262													6	3	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	58306	58308	+	Intron	DEL	TAT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58306_58308delTAT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TACATTGAGCTATTATTCTATAT	0.296													3	3	---	---	---	---	
NOP14	8602	broad.mit.edu	37	4	2953837	2953837	+	Intron	DEL	A	-	-	rs34128991		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2953837delA	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_Intron|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						tgtctcaaagaaaaaaaaaaa	0.129													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3575371	3575372	+	IGR	INS	-	GG	GG	rs13135265		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3575371_3575372insGG								LRPAP1 (41147 upstream) : ADRA2C (192703 downstream)																							gggtgtgacacgtgggagaggg	0.104													4	3	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6339543	6339551	+	Intron	DEL	TCGGGCATT	-	-	rs140706990		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6339543_6339551delTCGGGCATT	uc003gjc.2	-						PPP2R2C_uc003gjb.2_Intron|PPP2R2C_uc011bwd.1_Intron|PPP2R2C_uc011bwe.1_Intron|PPP2R2C_uc003gja.2_Intron|PPP2R2C_uc003gjd.1_Intron	NM_020416	NP_065149	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						CTGGCTGTACTCGGGCATTTCTGAGGGTT	0.450													2	4	---	---	---	---	
WDR1	9948	broad.mit.edu	37	4	10089385	10089385	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10089385delC	uc003gmf.2	-	8	1180	c.897delG	c.(895-897)GGGfs	p.G299fs	WDR1_uc003gmg.2_Frame_Shift_Del_p.G159fs|WDR1_uc003gmh.1_RNA|WDR1_uc011bwu.1_Frame_Shift_Del_p.G134fs	NM_017491	NP_059830	O75083	WDR1_HUMAN	WD repeat-containing protein 1 isoform 1	299					platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		AGTTGATGTACCCGGACAGGG	0.607													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10125815	10125816	+	5'Flank	INS	-	A	A	rs139342610	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10125815_10125816insA	uc003gmm.2	+											DQ573667																		cttccctgtttaaaggacactg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12452177	12452177	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12452177delA								None (None upstream) : HSP90AB2P (882860 downstream)																							ctggagtgagaaaaaaaaatg	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14370201	14370201	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14370201delT								BOD1L (740873 upstream) : CPEB2 (635321 downstream)																							cttctgaccgttttttggcag	0.000													4	2	---	---	---	---	
PPARGC1A	10891	broad.mit.edu	37	4	23802814	23802817	+	Intron	DEL	ACAC	-	-	rs34293917		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23802814_23802817delACAC	uc003gqs.2	-						PPARGC1A_uc003gqt.2_Intron	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor						androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)				CAGGTTACAAacacacacacacac	0.196													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	36268179	36268182	+	Intron	DEL	CCTC	-	-	rs140197823	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36268179_36268182delCCTC	uc003gss.2	+						uc010ifa.1_Intron					Homo sapiens cDNA clone IMAGE:4799398.																		ttccttcattcctccctccctccc	0.216													4	2	---	---	---	---	
RELL1	768211	broad.mit.edu	37	4	37605178	37605178	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37605178delC	uc003gsz.2	-							NM_001085399	NP_001078868	Q8IUW5	RELL1_HUMAN	receptor expressed in lymphoid tissues like 1							cytoplasm|integral to membrane|microtubule cytoskeleton|plasma membrane					0						GACGCCATTTCCAAGCCCCCA	0.488											OREG0016149	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42758534	42758535	+	IGR	INS	-	C	C	rs139948280	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42758534_42758535insC								ATP8A1 (99412 upstream) : GRXCR1 (136749 downstream)																							tgttcaacaaactggcaaaaac	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49237605	49237606	+	5'Flank	DEL	AT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49237605_49237606delAT	uc003gyy.2	-											DQ587539																		CTGAACTGACATGTGTATATAC	0.371													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49318804	49318804	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49318804delG								CWH43 (254711 upstream) : None (None downstream)																							ccaaccctcagggactctcct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57636025	57636025	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57636025delA								HOPX (88153 upstream) : SPINK2 (40009 downstream)																							ctctctctacaaaaaaaatag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70249344	70249346	+	IGR	DEL	AGA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70249344_70249346delAGA								UGT2B28 (88577 upstream) : UGT2B4 (96538 downstream)																							cctagatttcagaagatttatgg	0.000													4	2	---	---	---	---	
CXCL13	10563	broad.mit.edu	37	4	78459676	78459677	+	Intron	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78459676_78459677delTG	uc003hkr.2	+							NM_006419	NP_006410	O43927	CXL13_HUMAN	chemokine (C-X-C motif) ligand 13 (B-cell						activation of Rap GTPase activity|B cell chemotaxis|cell-cell signaling|chronic inflammatory response|defense response to bacterium|elevation of cytosolic calcium ion concentration|endothelial cell chemotaxis to fibroblast growth factor|germinal center formation|lymphocyte chemotaxis across high endothelial venule|negative regulation of apoptosis|positive regulation of cell-cell adhesion mediated by integrin|positive regulation of integrin activation|positive regulation of T cell chemotaxis|regulation of angiogenesis|regulation of humoral immune response	extracellular space|soluble fraction	CCR10 chemokine receptor binding|chemokine activity|CXCR3 chemokine receptor binding|CXCR5 chemokine receptor binding|fibroblast growth factor 2 binding|heparin binding|protein heterodimerization activity|receptor agonist activity				0						CTTCCACTTCTGTACTATAGAA	0.386													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91721864	91721864	+	Intron	DEL	T	-	-	rs5860204		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91721864delT	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						TCCAAATCGATTTTTAATGAA	0.328													4	2	---	---	---	---	
PPP3CA	5530	broad.mit.edu	37	4	102010411	102010412	+	Intron	INS	-	A	A	rs137876421	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102010411_102010412insA	uc011cen.1	-						PPP3CA_uc003hvu.2_Intron|PPP3CA_uc010ilj.2_Intron|PPP3CA_uc003hvt.2_Intron|PPP3CA_uc003hvs.2_Intron|PPP3CA_uc010ilk.2_Intron	NM_000944	NP_000935	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha						protein dephosphorylation	calcineurin complex|cytosol|nucleus	calcium ion binding|calmodulin binding			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		AGAAGAAAGACAAAAAAAAAGA	0.431													4	2	---	---	---	---	
BANK1	55024	broad.mit.edu	37	4	102647685	102647685	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102647685delG	uc003hvx.3	+							NM_001083907	NP_001077376	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		ATTGTTTGGTGGACAAATGTA	0.348													4	2	---	---	---	---	
TACR3	6870	broad.mit.edu	37	4	104537459	104537460	+	Intron	INS	-	TG	TG	rs142553092	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104537459_104537460insTG	uc003hxe.1	-							NM_001059	NP_001050	P29371	NK3R_HUMAN	tachykinin receptor 3							integral to plasma membrane	tachykinin receptor activity			ovary(3)|lung(2)|breast(1)|skin(1)	7		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		ACATACgtgtatgtgtgtgtgt	0.188													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104969837	104969838	+	IGR	DEL	CT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104969837_104969838delCT								TACR3 (328864 upstream) : CXXC4 (423507 downstream)																							tgactctctcctctctctctct	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	107287096	107287099	+	IGR	DEL	ACAC	-	-	rs113540116		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107287096_107287099delACAC								AIMP1 (16717 upstream) : DKK2 (555861 downstream)																							acacacacgtacacacacacacac	0.324													4	2	---	---	---	---	
ELOVL6	79071	broad.mit.edu	37	4	111049198	111049198	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111049198delA	uc003hzz.2	-						ELOVL6_uc003iaa.2_Intron	NM_001130721	NP_001124193	Q9H5J4	ELOV6_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, saturated fatty acid|long-chain fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process		fatty acid elongase activity|protein binding			haematopoietic_and_lymphoid_tissue(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		atcctgtctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
ANK2	287	broad.mit.edu	37	4	113772786	113772786	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113772786delT	uc003ibd.3	+						ANK2_uc003ibc.2_Intron	NM_001127493	NP_001120965	Q01484	ANK2_HUMAN	ankyrin 2 isoform 3						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		tttctttttcttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118907361	118907361	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118907361delA								TRAM1L1 (900625 upstream) : NDST3 (47412 downstream)																							CAAATAGGGGAAGGCACAGAT	0.473													4	2	---	---	---	---	
PRDM5	11107	broad.mit.edu	37	4	121655399	121655402	+	Intron	DEL	TTTG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121655399_121655402delTTTG	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron	NM_018699	NP_061169	Q9NQX1	PRDM5_HUMAN	PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2						GGGGGAGGGCTTTGTTTGTTTGTT	0.485													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	147555018	147555018	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147555018delC								SLC10A7 (111895 upstream) : POU4F2 (5027 downstream)																							GAGGCGGTTACCCTCGGGCAT	0.552													4	4	---	---	---	---	
PDGFC	56034	broad.mit.edu	37	4	157846149	157846149	+	Intron	DEL	T	-	-	rs77802931		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157846149delT	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		gggctgggcCTTGCAGGAGGC	0.199													4	2	---	---	---	---	
FNIP2	57600	broad.mit.edu	37	4	159689468	159689473	+	5'Flank	DEL	TGTGTG	-	-	rs71587478		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159689468_159689473delTGTGTG	uc003iqe.3	+						FNIP2_uc003iqd.2_5'Flank	NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TAGTGAGTTCtgtgtgtgtgtgtgtg	0.262													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190543358	190543358	+	IGR	DEL	T	-	-	rs35986093		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190543358delT								None (None upstream) : FRG1 (318616 downstream)																							CATGAATGCATTTTCTCTAAC	0.348													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190567803	190567805	+	IGR	DEL	ACA	-	-	rs66528226		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190567803_190567805delACA								None (None upstream) : FRG1 (294169 downstream)																							CCGTCCAAACACAACAGTTGCTA	0.517													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190567934	190567935	+	IGR	INS	-	T	T	rs144000523		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190567934_190567935insT								None (None upstream) : FRG1 (294039 downstream)																							AATATGGTGACTCTGACGGCTG	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190620208	190620209	+	IGR	INS	-	TAT	TAT	rs139963892		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190620208_190620209insTAT								None (None upstream) : FRG1 (241765 downstream)																							ccggccAGTAATTTTACTCTGT	0.163													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190821799	190821800	+	Intron	INS	-	T	T	rs140638219	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190821799_190821800insT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		TTTTTTGTTTGTTTTTTACTTA	0.317													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190837765	190837765	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190837765delA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		acacagtgagaccttgtccct	0.154													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190894272	190894273	+	IGR	DEL	AT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190894272_190894273delAT								FRG1 (9914 upstream) : TUBB4Q (9406 downstream)																							ACCATAAAAGATATGTAGGCTG	0.198													3	3	---	---	---	---	
PLEKHG4B	153478	broad.mit.edu	37	5	139431	139431	+	5'Flank	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139431delA	uc003jak.2	+							NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(2)	2			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		TTCTAGTCCTAATGACCTGCT	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1192038	1192039	+	IGR	INS	-	A	A	rs71593143		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1192038_1192039insA								SLC12A7 (79866 upstream) : SLC6A19 (9671 downstream)																							ggccgaggagtggggaagatgt	0.243													4	2	---	---	---	---	
IRX4	50805	broad.mit.edu	37	5	1881434	1881435	+	Intron	INS	-	T	T	rs143666424	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1881434_1881435insT	uc003jcz.2	-						IRX4_uc011cmf.1_Intron	NM_016358	NP_057442	P78413	IRX4_HUMAN	iroquois homeobox 4						heart development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(108;0.242)		ggcgcaaggcggggggaggagc	0.005													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1908847	1908848	+	IGR	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1908847_1908848delCA								IRX4 (25967 upstream) : IRX2 (837433 downstream)																							catgcacacgcacacacacaca	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2147577	2147577	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2147577delT								IRX4 (264697 upstream) : IRX2 (598704 downstream)																							TCTCAATGACttttttttttt	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3521157	3521157	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3521157delA	uc003jdd.2	-											Homo sapiens cDNA clone IMAGE:4823480.																		caacaaagtcaaaaaaaggaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4977980	4977981	+	IGR	DEL	TG	-	-	rs35730416		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4977980_4977981delTG								None (None upstream) : LOC340094 (56491 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.347													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5367705	5367706	+	IGR	DEL	CA	-	-	rs10574110		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5367705_5367706delCA								ADAMTS16 (47294 upstream) : KIAA0947 (55101 downstream)																							caaacgcgcgcacacacacaca	0.292													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5758843	5758844	+	IGR	DEL	TG	-	-	rs58588082		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5758843_5758844delTG								KIAA0947 (268506 upstream) : FLJ33360 (551710 downstream)																							TAGTGgtgtctgtgtgtgtgtg	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6116396	6116399	+	IGR	DEL	GTGT	-	-	rs3041062		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6116396_6116399delGTGT								KIAA0947 (626059 upstream) : FLJ33360 (194155 downstream)																							TACTAATAGCgtgtgtgtgtgtgt	0.196													4	2	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7593918	7593918	+	Intron	DEL	A	-	-	rs151256440	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7593918delA	uc003jdz.1	+							NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						gacaaacgtgaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7994364	7994364	+	IGR	DEL	C	-	-	rs35819821		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7994364delC								MTRR (93131 upstream) : None (None downstream)																							AGCATATGGGCTAGTGCATCG	0.378													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8269709	8269710	+	IGR	DEL	TG	-	-	rs112019808		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8269709_8269710delTG								MTRR (368476 upstream) : SEMA5A (765428 downstream)																							tgcgtgtgtttgtgtgtgtgtg	0.386													4	3	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9477032	9477032	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9477032delA	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						ttacaaaactaaaaaaaaaaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10139569	10139569	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10139569delT								LOC285692 (235633 upstream) : FAM173B (86869 downstream)																							GGTTATGACCTTTTCTCAAAA	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	12408224	12408224	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12408224delC								CTNND2 (504114 upstream) : None (None downstream)																							ttttttttttccccaaataga	0.000													4	2	---	---	---	---	
TRIO	7204	broad.mit.edu	37	5	14380641	14380642	+	Intron	INS	-	A	A	rs141366477	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14380641_14380642insA	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					GTCCCTTCCTGAAAAGGCTCAT	0.470													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18394355	18394355	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18394355delT								None (None upstream) : None (None downstream)																							cacggggccctttctttgtta	0.139											OREG0016537	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	21845665	21845667	+	Intron	DEL	TTT	-	-	rs35128409		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21845665_21845667delTTT	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						CACTTTAGTCTTTTTTTTTTTTT	0.419										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23686906	23686906	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23686906delG								PRDM9 (158202 upstream) : CDH10 (800304 downstream)																							CCAGGGCcatggcagagcatc	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	26230897	26230898	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26230897_26230898insT								None (None upstream) : CDH9 (649811 downstream)																							tccttcctttctttctttcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	35944870	35944870	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35944870delG								CAPSL (5989 upstream) : UGT3A1 (8340 downstream)																							AGTGTTATTTGGGAGCTGAAG	0.433													4	2	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38300478	38300478	+	Intron	DEL	T	-	-	rs34070893		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38300478delT	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					tctctctctcttttttttttt	0.000													4	2	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38449219	38449220	+	Intron	INS	-	C	C	rs143929233	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38449219_38449220insC	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_Intron|EGFLAM_uc003jlf.1_Intron|EGFLAM_uc003jlg.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					TTCTTTCCCTTCCCCAGTTCTT	0.450													5	5	---	---	---	---	
FYB	2533	broad.mit.edu	37	5	39182239	39182242	+	Intron	DEL	CTAA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39182239_39182242delCTAA	uc003jls.2	-						FYB_uc003jlt.2_Intron|FYB_uc003jlu.2_Intron|FYB_uc011cpl.1_Intron	NM_199335	NP_955367	O15117	FYB_HUMAN	FYN binding protein (FYB-120/130) isoform 2						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)			cggttcctgcctaactaactcccc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39552200	39552201	+	IGR	INS	-	TG	TG	rs139240644	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39552200_39552201insTG								DAB2 (126865 upstream) : None (None downstream)																							TATATATGTCATGTGTGTGTGT	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42017880	42017881	+	IGR	INS	-	T	T	rs35881762		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42017880_42017881insT								FBXO4 (76217 upstream) : GHR (406145 downstream)																							gatttcctgccttttttttttt	0.000													4	2	---	---	---	---	
ZNF131	7690	broad.mit.edu	37	5	43165308	43165308	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43165308delT	uc011cpw.1	+						ZNF131_uc003jnj.3_Intron|ZNF131_uc003jnk.2_Intron|ZNF131_uc003jnn.3_Intron|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron	NM_003432	NP_003423	P52739	ZN131_HUMAN	zinc finger protein 131							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CCTGTATTTCTTTTTTTTTTT	0.104													4	2	---	---	---	---	
MGC42105	167359	broad.mit.edu	37	5	43242908	43242908	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43242908delT	uc003jno.2	+							NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9						cACCTGGTGCttttttttttt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43525346	43525346	+	IGR	DEL	G	-	-	rs5867635		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43525346delG								C5orf34 (10159 upstream) : PAIP1 (1026 downstream)																							CTTTCATTATGTACTGGTGTA	0.433													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	46093974	46093974	+	IGR	DEL	T	-	-	rs143907956		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46093974delT								HCN1 (397754 upstream) : None (None downstream)																							ttggaaacagtttttttttgt	0.000													4	6	---	---	---	---	
CDK7	1022	broad.mit.edu	37	5	68544893	68544894	+	Intron	DEL	CT	-	-	rs6874496	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68544893_68544894delCT	uc003jvs.3	+						CDK7_uc010ixd.1_Intron|CDK7_uc003jvt.3_Intron|CDK7_uc003jvu.3_Intron	NM_001799	NP_001790	P50613	CDK7_HUMAN	cyclin-dependent kinase 7						androgen receptor signaling pathway|cell division|cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex|mitochondrion	androgen receptor binding|ATP binding|cyclin-dependent protein kinase activity|DNA-dependent ATPase activity|protein C-terminus binding|RNA polymerase II carboxy-terminal domain kinase activity|transcription coactivator activity			lung(1)	1		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)		tcttctttgcctctctctctct	0.000								NER					5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73354355	73354355	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73354355delT								RGNEF (116942 upstream) : ENC1 (568880 downstream)																							gagcatccccttttttgaacg	0.060													4	2	---	---	---	---	
EDIL3	10085	broad.mit.edu	37	5	83440058	83440058	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83440058delG	uc003kio.1	-						EDIL3_uc003kip.1_Intron	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		ttctttccttgcctcccttcc	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96576134	96576134	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96576134delT								RIOK2 (57129 upstream) : None (None downstream)																							ctcGGGACTCTTTTTTTTTTT	0.164													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116516172	116516173	+	IGR	INS	-	AAC	AAC	rs138946024	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116516172_116516173insAAC								SEMA6A (605621 upstream) : None (None downstream)																							ctagacaaaataacaacaacaa	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	122410911	122410912	+	IGR	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122410911_122410912insA								PPIC (38486 upstream) : PRDM6 (13929 downstream)																							GACCTTGAAACAAAAAAAACAC	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133089326	133089327	+	IGR	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133089326_133089327delTG								FSTL4 (141103 upstream) : C5orf15 (201872 downstream)																							tgaccctgcctggacttatccc	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141476477	141476477	+	IGR	DEL	T	-	-	rs11326201		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141476477delT								GNPDA1 (83857 upstream) : NDFIP1 (11847 downstream)																							ACCCCGAttcttttttttttt	0.234													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163302988	163302988	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163302988delT								MAT2B (356655 upstream) : None (None downstream)																							aatttttgtattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163360779	163360779	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163360779delA								MAT2B (414446 upstream) : None (None downstream)																							catcatcaagaaaaaaggcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165110254	165110254	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165110254delA								None (None upstream) : None (None downstream)																							ctaaaaacgtaaattcaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172673980	172673980	+	IGR	DEL	A	-	-	rs5873351		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172673980delA								NKX2-5 (11718 upstream) : STC2 (67746 downstream)																							AGCCTTAGTTAAAAAAAAAAA	0.368													3	3	---	---	---	---	
FAM153B	202134	broad.mit.edu	37	5	175523640	175523640	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175523640delC	uc003mdk.2	+						FAM153B_uc010jjy.1_Intron	NM_001079529	NP_001072997	P0C7A2	F153B_HUMAN	hypothetical protein LOC202134											ovary(1)	1	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		GCTCTGTCTTCCGTGGCTTTC	0.507													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179897146	179897149	+	IGR	DEL	TTTC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179897146_179897149delTTTC								GFPT2 (116831 upstream) : CNOT6 (24268 downstream)																							ttcttttctatttctttctttctt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180708776	180708777	+	IGR	INS	-	G	G	rs140221514		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180708776_180708777insG								TRIM52 (20657 upstream) : None (None downstream)																							gggcggtaggagggggctggag	0.144													4	2	---	---	---	---	
LOC285768	285768	broad.mit.edu	37	6	1053912	1053917	+	Intron	DEL	CAGAAG	-	-	rs113660342		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1053912_1053917delCAGAAG	uc011dhp.1	-						LOC285768_uc010jnf.1_Intron|LOC285768_uc003mtj.2_Intron	NR_027115				Homo sapiens cDNA clone IMAGE:5272115.												0						AACAGCAACACAGAAGTAGACATAGA	0.383													4	3	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	2203894	2203894	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2203894delA	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		TAACACTACGAAAAAAAAATG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3461935	3461936	+	IGR	INS	-	ACACAC	ACACAC	rs140731703	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3461935_3461936insACACAC								SLC22A23 (5142 upstream) : C6orf145 (260900 downstream)																							aaTGTTCTTTGacacacacaca	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8144687	8144687	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8144687delA								EEF1E1 (41859 upstream) : SLC35B3 (267046 downstream)																							TGAAGGATGGAAAAAGGAagg	0.164													4	2	---	---	---	---	
GMPR	2766	broad.mit.edu	37	6	16264656	16264656	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16264656delG	uc003nbs.2	+							NM_006877	NP_006868	P36959	GMPR1_HUMAN	guanosine monophosphate reductase						nucleotide metabolic process|purine base metabolic process|purine-containing compound salvage|response to cold	cytosol	GMP reductase activity|metal ion binding			ovary(1)	1	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				aagagcaggaggacaggggat	0.000													4	2	---	---	---	---	
KIF13A	63971	broad.mit.edu	37	6	17906684	17906685	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17906684_17906685insT	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			tttctttcttcttttttttttt	0.020													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26682200	26682202	+	IGR	DEL	GTA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26682200_26682202delGTA								ZNF322A (22237 upstream) : GUSBL1 (157064 downstream)																							GTTTCCTAAGGTAGTGGTCAGCA	0.453													6	3	---	---	---	---	
GPX6	257202	broad.mit.edu	37	6	28474483	28474484	+	Intron	INS	-	AC	AC	rs56155284		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28474483_28474484insAC	uc011dlj.1	-						GPX6_uc010jrg.1_Intron	NM_182701	NP_874360	P59796	GPX6_HUMAN	glutathione peroxidase 6 precursor						response to oxidative stress	extracellular region	glutathione peroxidase activity			ovary(3)|pancreas(1)|skin(1)	5					Glutathione(DB00143)	TTTTTTTTTAAacacacacaca	0.342													1	5	---	---	---	---	
COL11A2	1302	broad.mit.edu	37	6	33149024	33149025	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33149024_33149025insA	uc003ocx.1	-						COL11A2_uc003ocy.1_Intron|COL11A2_uc003ocz.1_Intron	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1						cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						ATCTCAACTCCAACCTTGATTC	0.579													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33810682	33810682	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33810682delG								MLN (38889 upstream) : MIR1275 (157067 downstream)																							ACCAGAAGGTGGAGGAGAGAA	0.612													4	2	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34039881	34039882	+	Intron	INS	-	CA	CA	rs148378602		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34039881_34039882insCA	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	tcaccacccaccacagatacac	0.000													4	2	---	---	---	---	
ANKS1A	23294	broad.mit.edu	37	6	34938628	34938628	+	Intron	DEL	A	-	-	rs62874061	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34938628delA	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron|ANKS1A_uc010jvq.1_Intron|ANKS1A_uc010jvr.1_5'Flank	NM_015245	NP_056060	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4						ataaaaaattaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38493021	38493022	+	Intron	INS	-	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38493021_38493022insC	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a						cell adhesion						0						taatcagttttccctgctcttg	0.000													4	2	---	---	---	---	
FAM83B	222584	broad.mit.edu	37	6	54792525	54792526	+	Intron	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54792525_54792526delGT	uc003pck.2	+							NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584											ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					TTTCTTAAAAGTaaaaaaaaaa	0.119													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57253252	57253254	+	Intron	DEL	ATA	-	-	rs147405680		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57253252_57253254delATA	uc003pdx.2	+						hsa-mir-548u|MI0014168_5'Flank	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		aagaatcaGCATAATGATGATGA	0.059													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57515828	57515828	+	IGR	DEL	C	-	-	rs11292500		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57515828delC								PRIM2 (2453 upstream) : GUSBL2 (730331 downstream)																							AAGCAAACTTCTGTAATTCTT	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57517009	57517010	+	IGR	INS	-	ATTTA	ATTTA	rs5876670		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57517009_57517010insATTTA								PRIM2 (3634 upstream) : GUSBL2 (729149 downstream)																							ACAAATACTGCATTTAAGACTG	0.356													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57525749	57525750	+	IGR	INS	-	C	C	rs149294374		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57525749_57525750insC								PRIM2 (12374 upstream) : GUSBL2 (720409 downstream)																							ttgattttttttgatgggctta	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57553541	57553542	+	IGR	DEL	AG	-	-	rs113085434		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57553541_57553542delAG								PRIM2 (40166 upstream) : GUSBL2 (692617 downstream)																							agtgacctacagagtcaatgca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57565371	57565372	+	IGR	INS	-	CTA	CTA	rs149489760		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57565371_57565372insCTA								PRIM2 (51996 upstream) : GUSBL2 (680787 downstream)																							GAATCTGGACCCTACTAGTCAG	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	72580395	72580396	+	IGR	DEL	AA	-	-	rs35309683		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72580395_72580396delAA								C6orf155 (449947 upstream) : RIMS1 (16254 downstream)																							ATTGTAGAAGAAAAAAAAAAAA	0.203													2	5	---	---	---	---	
IRAK1BP1	134728	broad.mit.edu	37	6	79580476	79580476	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79580476delG	uc003pim.2	+						IRAK1BP1_uc010kbg.1_Intron|IRAK1BP1_uc003pin.2_5'Flank	NM_001010844	NP_001010844	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1						I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus					0		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		cgcccaggctggagtacaatg	0.065													4	2	---	---	---	---	
RARS2	57038	broad.mit.edu	37	6	88267899	88267900	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88267899_88267900insA	uc003pme.2	-						RARS2_uc003pmb.2_Intron|RARS2_uc003pmc.2_Intron|RARS2_uc003pmd.2_Intron|RARS2_uc003pmf.2_Intron	NM_020320	NP_064716	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial						arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		ccgtctcaaagaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92651100	92651101	+	IGR	DEL	AA	-	-	rs141031400		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92651100_92651101delAA								None (None upstream) : None (None downstream)																							CCAAGAACTCaaaaaaaaaaaa	0.297													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	94850681	94850681	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94850681delT								TSG1 (364482 upstream) : None (None downstream)																							TCAGGAtttcttttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	101710029	101710029	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101710029delT								ASCC3 (380805 upstream) : GRIK2 (136876 downstream)																							agtgctgggattacaggcttg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	106138101	106138102	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106138101_106138102insT								PREP (287132 upstream) : PRDM1 (396093 downstream)																							aaaaaccacaattacttttgca	0.203													4	2	---	---	---	---	
MICAL1	64780	broad.mit.edu	37	6	109769301	109769302	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109769301_109769302delAC	uc003ptj.2	-						MICAL1_uc003ptk.2_Intron|MICAL1_uc010kdr.2_Intron|MICAL1_uc011eaq.1_Intron	NM_022765	NP_073602	Q8TDZ2	MICA1_HUMAN	microtubule associated monoxygenase, calponin						cytoskeleton organization|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding			breast(2)|ovary(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		CCTCTTTCTGacacacacacac	0.446													9	4	---	---	---	---	
RPF2	84154	broad.mit.edu	37	6	111319103	111319104	+	Intron	DEL	TT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111319103_111319104delTT	uc003pun.2	+						RPF2_uc003puo.2_Intron	NM_032194	NP_115570	Q9H7B2	RPF2_HUMAN	brix domain containing 1							nucleolus	protein binding			ovary(2)	2						tcttttcttctttttttttttt	0.000													4	2	---	---	---	---	
TRDN	10345	broad.mit.edu	37	6	123585820	123585821	+	Intron	INS	-	AAAG	AAAG	rs142372294	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123585820_123585821insAAAG	uc003pzj.1	-						TRDN_uc010kem.1_Intron	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		aatcttttgtcagtcaatcaat	0.000													4	3	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	125003083	125003083	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125003083delA	uc003pzo.2	+						NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		AGAAACCATGAAAGAAAGGAA	0.353													4	2	---	---	---	---	
TMEM200A	114801	broad.mit.edu	37	6	130757102	130757102	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130757102delC	uc003qca.2	+						TMEM200A_uc010kfh.2_Intron|TMEM200A_uc010kfi.2_Intron|TMEM200A_uc003qcb.2_5'Flank	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A							integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		CTTATGTACTCCCCATGGCTT	0.458													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134791949	134791950	+	Intron	INS	-	TC	TC	rs147459730	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134791949_134791950insTC	uc003qeq.1	-						uc003qer.1_Intron|uc003qes.1_Intron|uc003qet.1_Intron|uc003qeu.1_Intron					Homo sapiens cDNA clone IMAGE:4837072.																		ctttctttctttctctctctct	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	135471486	135471486	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135471486delT								HBS1L (95450 upstream) : MYB (30967 downstream)																							tttttctttcttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	140697641	140697641	+	IGR	DEL	C	-	-	rs66733950		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140697641delC								None (None upstream) : None (None downstream)																							ctttctttctccccccccttt	0.020													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141511912	141511913	+	IGR	INS	-	T	T	rs138488600	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141511912_141511913insT								None (None upstream) : NMBR (884833 downstream)																							ataaagtttaatttttttttct	0.000													2	4	---	---	---	---	
LOC153910	153910	broad.mit.edu	37	6	142909365	142909366	+	Intron	INS	-	AC	AC	rs143628888	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142909365_142909366insAC	uc003qjc.1	-						LOC153910_uc010khg.1_Intron	NR_027312				Homo sapiens cDNA FLJ31371 fis, clone NB9N42000196.												0						aaaaaaaaatgacagtgcacaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145325228	145325229	+	IGR	INS	-	CCA	CCA	rs141195493	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145325228_145325229insCCA								UTRN (151060 upstream) : EPM2A (621217 downstream)																							tggttctccttccacctctctg	0.208													4	3	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	151036611	151036612	+	Intron	INS	-	T	T	rs145273046	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151036611_151036612insT	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GTTCATCACTAttttttttctt	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156062241	156062242	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156062241_156062242insT								NOX3 (285204 upstream) : MIR1202 (205689 downstream)																							tccttccttccttcctttcctt	0.045													5	4	---	---	---	---	
IGF2R	3482	broad.mit.edu	37	6	160524351	160524352	+	Intron	INS	-	A	A	rs78919467		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160524351_160524352insA	uc003qta.2	+							NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor						receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)		agactctgtccaaaaaaaaaaa	0.317													2	4	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2035867	2035868	+	Intron	INS	-	C	C	rs146338923		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2035867_2035868insC	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GCGGGCAGGGTCCCCCCGGGTC	0.738													1	5	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	4196989	4196991	+	Intron	DEL	GTG	-	-	rs9297132	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4196989_4196991delGTG	uc003smx.2	+						SDK1_uc010kso.2_Intron|SDK1_uc003smy.2_Intron	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		aggaaggaaagtgggaagggagg	0.000													4	2	---	---	---	---	
ZNF12	7559	broad.mit.edu	37	7	6742671	6742672	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6742671_6742672delAC	uc003sqt.1	-						ZNF12_uc011jxa.1_Intron|ZNF12_uc003sqs.1_Intron	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		CTCCCAAACTacacacacacac	0.193													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	19988343	19988343	+	IGR	DEL	T	-	-	rs66954164		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19988343delT								TMEM196 (175127 upstream) : MACC1 (185945 downstream)																							AGAAGTACTCTtttttttttt	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36027639	36027639	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36027639delA								SEPT7 (82724 upstream) : EEPD1 (165197 downstream)																							AATCTTAAGCAAAAAAAAAAA	0.488													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36819735	36819736	+	IGR	DEL	AG	-	-	rs143709766		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36819735_36819736delAG								AOAH (55582 upstream) : ELMO1 (74225 downstream)																							aatgtaagacagagttttaaaa	0.000													4	3	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43235812	43235812	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43235812delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						ACTGTTCTCCTTCCTCTCCAA	0.274													4	2	---	---	---	---	
CAMK2B	816	broad.mit.edu	37	7	44294369	44294375	+	Intron	DEL	ACCAACT	-	-	rs111901158		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44294369_44294375delACCAACT	uc003tkq.2	-						CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron	NM_001220	NP_001211	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2						catcaccaccaccaactaccaccatca	0.029													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56635193	56635193	+	IGR	DEL	T	-	-	rs34132430		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56635193delT								DKFZp434L192 (70216 upstream) : ZNF479 (552135 downstream)																							CCTAGAAGTCTTAATGGCTTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56661642	56661642	+	IGR	DEL	A	-	-	rs34449118		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56661642delA								DKFZp434L192 (96665 upstream) : ZNF479 (525686 downstream)																							GTTTCTACATAAAAAAAGCTA	0.274													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57627797	57627797	+	IGR	DEL	G	-	-	rs77883576		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57627797delG								ZNF716 (94532 upstream) : None (None downstream)																							AAAAAGGTTTGGGCATTATTC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57659470	57659471	+	IGR	DEL	TA	-	-	rs79867563	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57659470_57659471delTA								ZNF716 (126205 upstream) : None (None downstream)																							GCGTTGATCTTACAGTCTGGTG	0.371													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57698975	57698976	+	IGR	INS	-	AGTG	AGTG	rs145904451	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57698975_57698976insAGTG								ZNF716 (165710 upstream) : None (None downstream)																							AAAAAATGTACAGTGAGGGAAT	0.277													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57774136	57774136	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57774136delT								ZNF716 (240871 upstream) : None (None downstream)																							aaactgccacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61095751	61095751	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61095751delT								None (None upstream) : None (None downstream)																							tgaaactttcttttgatagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61757015	61757015	+	IGR	DEL	G	-	-	rs139696463		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61757015delG								None (None upstream) : LOC643955 (994657 downstream)																							ggaatcgaatggaagcatcga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62648410	62648411	+	IGR	DEL	TG	-	-	rs145058899	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62648410_62648411delTG								None (None upstream) : LOC643955 (103261 downstream)																							TCTCTCCATATGcacacacaca	0.248													4	2	---	---	---	---	
CRCP	27297	broad.mit.edu	37	7	65599533	65599533	+	Intron	DEL	T	-	-	rs146459004		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65599533delT	uc003tus.2	+						CRCP_uc003tuv.2_Intron|CRCP_uc011kdw.1_Intron|CRCP_uc003tut.2_Intron|CRCP_uc003tuu.2_Intron	NM_014478	NP_055293	O75575	RPC9_HUMAN	calcitonin gene-related peptide-receptor						acrosome reaction|innate immune response|response to virus|transcription from RNA polymerase III promoter	DNA polymerase III complex|nucleus|plasma membrane	calcitonin receptor activity|DNA-directed RNA polymerase activity|nucleotide binding				0						GGAACAAATCttttttttttt	0.299													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67672966	67672966	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67672966delT								STAG3L4 (886454 upstream) : None (None downstream)																							agcttggagcttttttttttt	0.000													4	2	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71259815	71259816	+	Intron	INS	-	CTGCAGG	CTGCAGG	rs141075441	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71259815_71259816insCTGCAGG	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				CTCACCTTTCCCTTCCTGCAAA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	72834472	72834473	+	IGR	DEL	GT	-	-	rs72020865		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72834472_72834473delGT								FKBP6 (61831 upstream) : FZD9 (13636 downstream)																							gtgtgtgtgcgtgtgtgtgtgt	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89523992	89523992	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89523992delA								ZNF804B (557648 upstream) : DPY19L2P4 (224722 downstream)																							TTTTAACTGTAAGTGCTCATT	0.299													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90742168	90742169	+	Intron	INS	-	GAGA	GAGA	rs148244277	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90742168_90742169insGAGA	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						gtgtatgtgtggagagagagag	0.287													4	2	---	---	---	---	
SGCE	8910	broad.mit.edu	37	7	94232465	94232465	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94232465delC	uc003unl.2	-						SGCE_uc003unk.2_Intron|SGCE_uc003unm.2_Intron|SGCE_uc003unn.2_Intron|SGCE_uc011kic.1_Intron|SGCE_uc011kid.1_Intron	NM_003919	NP_003910	O43556	SGCE_HUMAN	sarcoglycan, epsilon isoform 2						cell-matrix adhesion|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CTTACCAGATCCTTAATCTCA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98116051	98116052	+	IGR	INS	-	G	G	rs142978910	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98116051_98116052insG								BAIAP2L1 (85624 upstream) : NPTX2 (130545 downstream)																							gtgcgtgtgtcgtatgggggcg	0.119													6	3	---	---	---	---	
AGFG2	3268	broad.mit.edu	37	7	100157807	100157807	+	Intron	DEL	T	-	-	rs113365559		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100157807delT	uc003uvf.2	+						AGFG2_uc010lgy.2_Intron	NM_006076	NP_006067	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1						TGCTGCTGGCttttttttttt	0.284													4	2	---	---	---	---	
EMID2	136227	broad.mit.edu	37	7	101196823	101196824	+	Intron	INS	-	T	T	rs66862056		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101196823_101196824insT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					acagccccatgggaactcagct	0.050													5	3	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101547397	101547398	+	Intron	INS	-	AC	AC	rs138765263	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101547397_101547398insAC	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						gtctttacaaaacacacacaca	0.000													3	3	---	---	---	---	
ATXN7L1	222255	broad.mit.edu	37	7	105498380	105498380	+	Intron	DEL	A	-	-	rs146876841		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105498380delA	uc003vde.2	-						ATXN7L1_uc003vdi.2_Intron	NM_020725	NP_065776	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1 isoform 1												0						CTACAGGGGGAAAAAAAAAAG	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109451493	109451493	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109451493delC								C7orf66 (926856 upstream) : EIF3IP1 (147791 downstream)																							cttttagattctttcctcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127268096	127268097	+	IGR	DEL	AG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127268096_127268097delAG								PAX4 (12114 upstream) : SND1 (24105 downstream)																							aaagaaagaaagaaaggaagaa	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	134374511	134374512	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134374511_134374512insT								BPGM (9946 upstream) : CALD1 (89659 downstream)																							TTTTAGTTTAAttttttttttt	0.005													4	2	---	---	---	---	
RAB19	401409	broad.mit.edu	37	7	140123960	140123960	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140123960delT	uc010lni.2	+						RAB19_uc011krc.1_Intron	NM_001008749	NP_001008749	A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0	Melanoma(164;0.0142)					tggcTGATAAttttttttttt	0.005													2	5	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146539142	146539142	+	Intron	DEL	T	-	-	rs67686633		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146539142delT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			gcctggctaatttttttttgt	0.000										HNSCC(39;0.1)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149343332	149343333	+	IGR	INS	-	AC	AC	rs140228604	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149343332_149343333insAC								ZNF767 (21451 upstream) : KRBA1 (68769 downstream)																							cacacacacaaacacacacaca	0.079													4	4	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153616601	153616601	+	Intron	DEL	A	-	-	rs79244820	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153616601delA	uc003wli.2	+							NM_001039350	NP_001034439	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 3						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TACTTTGATGAAAAAAAATGT	0.363													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155076912	155076912	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155076912delG								HTR5A (199453 upstream) : INSIG1 (12574 downstream)																							CAGGCAGCCTGGGGAGCCAGG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155739522	155739525	+	IGR	DEL	TTCC	-	-	rs5888641		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155739522_155739525delTTCC								SHH (134555 upstream) : C7orf4 (593660 downstream)																							ccttccttctttccttccttcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156170736	156170736	+	IGR	DEL	A	-	-	rs34568540		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156170736delA								SHH (565769 upstream) : C7orf4 (162449 downstream)																							actccatctcaaaaaaaaaaa	0.199													4	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158108215	158108216	+	Intron	INS	-	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158108215_158108216insC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TGAACCCGGGACCCCTGAAGGA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	158423275	158423275	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158423275delT								PTPRN2 (42793 upstream) : NCAPG2 (728 downstream)																							ATTTCTTTACTTTTTTGCTCA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1684758	1684758	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1684758delA								DLGAP2 (28118 upstream) : CLN8 (27112 downstream)																							accgtgtctcaaaaaaaaaaG	0.134													5	3	---	---	---	---	
GFRA2	2675	broad.mit.edu	37	8	21605269	21605270	+	Intron	DEL	CA	-	-	rs147214068		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21605269_21605270delCA	uc003wzu.1	-						GFRA2_uc003wzv.1_Intron|GFRA2_uc003wzw.1_Intron|DOK2_uc003wzx.1_Intron	NM_001495	NP_001486	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2 isoform a							anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity				0				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		CATCTTCCACcacacacacaca	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37593486	37593487	+	Frame_Shift_Ins	INS	-	A	A	rs112819064		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37593486_37593487insA	uc003xkb.1	-	2	878_879	c.529_530insT	c.(529-531)TCTfs	p.S177fs	ERLIN2_uc003xkc.3_5'Flank|ERLIN2_uc003xkd.2_5'Flank|ERLIN2_uc003xke.3_5'Flank|ERLIN2_uc003xkf.3_5'Flank|ERLIN2_uc003xkg.2_5'Flank					SubName: Full=Putative uncharacterized protein ENSP00000328874;																		ATCAAGGAGAGAAAAAAAAAAA	0.203													4	2	---	---	---	---	
BAG4	9530	broad.mit.edu	37	8	38040506	38040508	+	Intron	DEL	ACC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38040506_38040508delACC	uc003xky.1	+						BAG4_uc003xkz.1_Intron	NM_004874	NP_004865	O95429	BAG4_HUMAN	BCL2-associated athanogene 4						anti-apoptosis|apoptosis|protein folding	cytoplasm|nucleus	receptor signaling protein activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				caatTACATAaccaccaccacca	0.064													4	4	---	---	---	---	
FGFR1	2260	broad.mit.edu	37	8	38291846	38291847	+	Intron	DEL	GC	-	-	rs57213852		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38291846_38291847delGC	uc003xlp.2	-						FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Intron|FGFR1_uc011lbs.1_Intron|FGFR1_uc011lbt.1_Intron|FGFR1_uc011lbu.1_Intron|FGFR1_uc011lbv.1_Intron|FGFR1_uc011lbw.1_Intron|FGFR1_uc011lbx.1_Intron|FGFR1_uc003xlv.2_Intron|FGFR1_uc003xlu.2_Intron|FGFR1_uc003xlw.1_Intron	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	TATTGCTGCTGCtttttttttt	0.193		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						19	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	38357102	38357103	+	IGR	INS	-	T	T	rs79819522		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38357102_38357103insT								FGFR1 (30750 upstream) : C8orf86 (11249 downstream)																							TCAGAGCATAAttttttttttt	0.020													6	6	---	---	---	---	
TACC1	6867	broad.mit.edu	37	8	38688146	38688149	+	Intron	DEL	AAGG	-	-	rs80290948		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38688146_38688149delAAGG	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_Intron	NM_006283	NP_006274	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			GACCTGAGACAAGGAAGCCCATTT	0.324													1	14	---	---	---	---	
PLEKHA2	59339	broad.mit.edu	37	8	38768762	38768763	+	Intron	INS	-	T	T	rs149132081	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38768762_38768763insT	uc003xmi.3	+						PLEKHA2_uc011lce.1_Intron	NM_021623	NP_067636	Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A						positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding				0		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			TGAACACtttcttttttttttg	0.223													3	3	---	---	---	---	
IDO2	169355	broad.mit.edu	37	8	39818468	39818469	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39818468_39818469insT	uc010lwy.1	+						IDO2_uc003xno.1_Intron	NM_194294	NP_919270	Q6ZQW0	I23O2_HUMAN	indoleamine-pyrrole 2,3 dioxygenase-like 1						tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2						cgcccagctaatttttttgtat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	41115075	41115075	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41115075delT								ZMAT4 (359732 upstream) : SFRP1 (4404 downstream)																							CAGTTCTGGGTTTTTTTtttt	0.204													4	2	---	---	---	---	
SFRP1	6422	broad.mit.edu	37	8	41166638	41166640	+	In_Frame_Del	DEL	GCT	-	-	rs3055861		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41166638_41166640delGCT	uc003xnt.2	-	1	341_343	c.39_41delAGC	c.(37-42)GCAGCC>GCC	p.13_14AA>A		NM_003012	NP_003003	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1 precursor	13_14				Missing (in Ref. 1 and 3).	brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			CACGCCCAGGGCTGCCCCGCGGC	0.764													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	41772591	41772592	+	IGR	INS	-	GT	GT	rs145946154	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41772591_41772592insGT								ANK1 (18311 upstream) : MYST3 (14406 downstream)																							ttcgcgtgtgcgtgtgtgtgtg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43808432	43808432	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43808432delT								POTEA (590104 upstream) : None (None downstream)																							tgaaccttcctttttgataga	0.000													7	4	---	---	---	---	
ST18	9705	broad.mit.edu	37	8	53212629	53212629	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53212629delT	uc003xra.2	-						ST18_uc003xrb.2_Intron|ST18_uc010lyb.2_Intron	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTGTAAATGGTTTTCAGCCTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55121316	55121317	+	IGR	INS	-	TT	TT	rs34162406		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55121316_55121317insTT								MRPL15 (60242 upstream) : SOX17 (249178 downstream)																							tggctggctaattttttttttt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55941526	55941527	+	IGR	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55941526_55941527delAC								RP1 (258995 upstream) : XKR4 (73490 downstream)																							acacacacatacacacacacac	0.361													4	2	---	---	---	---	
PLAG1	5324	broad.mit.edu	37	8	57123388	57123388	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57123388delT	uc003xsr.3	-						PLAG1_uc010lyi.2_Intron|PLAG1_uc010lyj.2_Intron|CHCHD7_uc003xss.2_5'Flank|CHCHD7_uc003xst.2_5'Flank|CHCHD7_uc003xsu.2_5'Flank|CHCHD7_uc003xsv.2_5'Flank|CHCHD7_uc003xsw.2_5'Flank|CHCHD7_uc003xsx.2_5'Flank	NM_002655	NP_002646	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding		CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3)	salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1)	129		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			TGAATAAAGGTTTTTTTTTTT	0.473			T	TCEA1|LIFR|CTNNB1|CHCHD7	salivary adenoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58094436	58094436	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58094436delT								IMPAD1 (188009 upstream) : C8orf71 (97666 downstream)																							TTGTGATAACttttttttttt	0.119													3	3	---	---	---	---	
TOX	9760	broad.mit.edu	37	8	59732837	59732837	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59732837delA	uc003xtw.1	-							NM_014729	NP_055544	O94900	TOX_HUMAN	thymus high mobility group box protein TOX							nucleus	DNA binding			kidney(2)|lung(1)|skin(1)	4		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				TCTGTACGTTAAAAAAAAAAA	0.244													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60512618	60512618	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60512618delG								TOX (480851 upstream) : CA8 (588805 downstream)																							ttaaagatgaggtatctgtga	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60560032	60560032	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60560032delT								TOX (528265 upstream) : CA8 (541391 downstream)																							CTTTTTTCTGTTTTTTTTTTT	0.458													4	2	---	---	---	---	
ASPH	444	broad.mit.edu	37	8	62497459	62497459	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62497459delA	uc003xuj.2	-						ASPH_uc011leg.1_Intron|ASPH_uc003xuo.2_Intron	NM_004318	NP_004309	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	CAATAAGTTCAAAACCACGCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64299711	64299711	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64299711delT	uc003xvb.1	-											Homo sapiens cDNA FLJ36051 fis, clone TESTI2018083.																		TGTGAGACTGTTTTTTTTTTC	0.244													4	2	---	---	---	---	
CYP7B1	9420	broad.mit.edu	37	8	65679879	65679880	+	Intron	INS	-	AGAAA	AGAAA	rs138819421	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65679879_65679880insAGAAA	uc003xvj.2	-							NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				ccaggttcatcggaaaggaaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	68771898	68771898	+	IGR	DEL	T	-	-	rs67736973		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68771898delT								CPA6 (113278 upstream) : PREX2 (92450 downstream)																							CATGACCAGCTCCTCAAGATA	0.468													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70027050	70027051	+	IGR	INS	-	CTAA	CTAA	rs144772166	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70027050_70027051insCTAA								C8orf34 (295794 upstream) : SULF1 (351808 downstream)																							catacctgcagctaactagcat	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75334541	75334542	+	IGR	DEL	TT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75334541_75334542delTT								GDAP1 (55208 upstream) : MIR2052 (283386 downstream)																							tctttctttctttctttctttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76131224	76131231	+	IGR	DEL	GGGAAGGA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76131224_76131231delGGGAAGGA								CRISPLD1 (184433 upstream) : HNF4G (188952 downstream)																							ggagagaagggggaaggagggaaggagg	0.024													5	7	---	---	---	---	
ZFHX4	79776	broad.mit.edu	37	8	77733763	77733764	+	Intron	INS	-	T	T	rs113052635		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77733763_77733764insT	uc003yav.2	+						ZFHX4_uc003yau.1_Intron|ZFHX4_uc003yaw.1_Intron	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			tctttctgagattttttttttt	0.010										HNSCC(33;0.089)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	77786256	77786257	+	IGR	DEL	TC	-	-	rs142705893		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77786256_77786257delTC								ZFHX4 (6736 upstream) : PEX2 (106239 downstream)																							cttcaccccttctctctctctc	0.000													3	3	---	---	---	---	
ZBTB10	65986	broad.mit.edu	37	8	81422875	81422878	+	Intron	DEL	GTGT	-	-	rs144657712	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81422875_81422878delGTGT	uc003ybx.3	+						ZBTB10_uc003ybv.3_Intron|ZBTB10_uc003ybw.3_Intron|ZBTB10_uc010lzt.2_Intron	NM_001105539	NP_001099009	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10 isoform						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			TGTGAAACCAgtgtgtgtgtgtgt	0.309													4	2	---	---	---	---	
CA13	377677	broad.mit.edu	37	8	86309303	86309304	+	Intron	DEL	GT	-	-	rs3989411		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86309303_86309304delGT	uc003ydf.1	+									Q8N1Q1	CAH13_HUMAN	Homo sapiens cDNA FLJ36434 fis, clone THYMU2012002.						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0						GAGCTGTGGAgtgtgtgtgtgt	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	90710160	90710160	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90710160delC								None (None upstream) : RIPK2 (59815 downstream)																							atgagtttttcagctttatca	0.000													4	2	---	---	---	---	
GEM	2669	broad.mit.edu	37	8	95274307	95274307	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95274307delC	uc003ygj.2	-						GEM_uc003ygi.2_Intron	NM_005261	NP_005252	P55040	GEM_HUMAN	GTP-binding mitogen-induced T-cell protein						cell surface receptor linked signaling pathway|immune response|small GTPase mediated signal transduction	internal side of plasma membrane	calmodulin binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding			lung(1)	1	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			ACTTGAAGCTCTGACCCCTAC	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96756298	96756298	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96756298delT								C8orf37 (474861 upstream) : GDF6 (398262 downstream)																							acacgaagtatttatcagagt	0.104													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	103054274	103054274	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103054274delA	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			CCTTGAGAGCAAATGTTGCCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	104090258	104090258	+	IGR	DEL	A	-	-	rs77198868		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104090258delA								ATP6V1C1 (4974 upstream) : C8orf56 (54934 downstream)																							TTCTTCTAGCAAAGGGAACCC	0.463													6	4	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104961353	104961355	+	Intron	DEL	AAA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104961353_104961355delAAA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_Intron	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			agactctgtcaaaaaaaaaaaaa	0.005										HNSCC(12;0.0054)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112060225	112060226	+	IGR	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112060225_112060226delGT								None (None upstream) : None (None downstream)																							actgagaagggtgtgtgtgtgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116741233	116741234	+	IGR	DEL	GA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116741233_116741234delGA								TRPS1 (60005 upstream) : EIF3H (915822 downstream)																							AAGAAGGAGCgagagagagaga	0.030													5	3	---	---	---	---	
EXT1	2131	broad.mit.edu	37	8	118993947	118993947	+	Intron	DEL	A	-	-	rs71569753		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118993947delA	uc003yok.1	-							NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			cagttctactaaaaaaaaaaa	0.000			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				4	2	---	---	---	---	
DEPDC6	64798	broad.mit.edu	37	8	121035484	121035485	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121035484_121035485insT	uc003yow.3	+						DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			cttttcttttcttttttttgtt	0.000													4	2	---	---	---	---	
ZHX2	22882	broad.mit.edu	37	8	123949128	123949128	+	Intron	DEL	C	-	-	rs5894649		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123949128delC	uc003ypk.1	+							NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			ccaataaaagccccagaatgg	0.000													2	4	---	---	---	---	
WDR67	93594	broad.mit.edu	37	8	124098428	124098429	+	Intron	INS	-	C	C	rs145686579	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124098428_124098429insC	uc003ypp.1	+						WDR67_uc011lig.1_Intron|WDR67_uc011lih.1_Intron|WDR67_uc003ypq.1_Intron|WDR67_uc003ypo.1_Intron	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1							centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			CCACGCTGCTACCCCTCCTCCC	0.396													1	5	---	---	---	---	
ATAD2	29028	broad.mit.edu	37	8	124355228	124355229	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124355228_124355229insT	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			catcatcatcattttttttttt	0.000													4	2	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125722928	125722931	+	Intron	DEL	TGTG	-	-	rs149769261		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125722928_125722931delTGTG	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			AGAGAATAACTGTGTGTAGCTCAT	0.539													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128343203	128343203	+	Intron	DEL	T	-	-	rs34781937		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128343203delT	uc003ysc.1	-						uc003ysd.1_Intron|LOC727677_uc003yse.1_Intron					Homo sapiens isolate DGPc1_8_exons1-2-3-4-6-8 unknown mRNA, alternatively spliced.																		GGCTATAGGATTTTTTTTTTC	0.383													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129743900	129743900	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129743900delT								MIR1208 (581466 upstream) : None (None downstream)																							actcaaacgatttatgtaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130014149	130014150	+	IGR	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130014149_130014150delAC								MIR1208 (851715 upstream) : GSDMC (746293 downstream)																							GAGGCAGATGACACACACACAC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130647440	130647440	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130647440delA								None (None upstream) : GSDMC (113003 downstream)																							ACTGAGAGATAAGGAGTATTG	0.408													4	2	---	---	---	---	
KCNQ3	3786	broad.mit.edu	37	8	133421708	133421708	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133421708delA	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			gatctcctgtaaaaaaaaaaa	0.080													4	2	---	---	---	---	
ST3GAL1	6482	broad.mit.edu	37	8	134535586	134535596	+	Intron	DEL	CTTTCTCCACC	-	-	rs111786791		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134535586_134535596delCTTTCTCCACC	uc003yuk.2	-						ST3GAL1_uc003yum.2_Intron	NM_173344	NP_775479	Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			GCAGCTGTTGCTTTCTCCACCCTTAGAAGCa	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134686570	134686570	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134686570delT								ST3GAL1 (102387 upstream) : ZFAT (803463 downstream)																							CATCAGCGCCTTTTGATTTCT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136414552	136414553	+	IGR	DEL	AG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136414552_136414553delAG								LOC286094 (102593 upstream) : KHDRBS3 (55163 downstream)																							gtgtgtacacagagagagagag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136737562	136737563	+	IGR	INS	-	TT	TT	rs72541519		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136737562_136737563insTT								KHDRBS3 (77716 upstream) : None (None downstream)																							TCTGTCCTCTCGGTAGAAAAGG	0.520													2	4	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139750989	139750990	+	Intron	INS	-	ATT	ATT			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139750989_139750990insATT	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GGCTCTGAAGAATTAAAAGGGA	0.267										HNSCC(7;0.00092)			4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139882630	139882631	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139882630_139882631insT	uc003yvd.2	-							NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TGTGCAGTGTGTGGGGTATGCA	0.153										HNSCC(7;0.00092)			4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	140767745	140767745	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140767745delA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						GGGTTGGGGTATAAGGACAGC	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144466709	144466709	+	IGR	DEL	C	-	-	rs35470357		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144466709delC								RHPN1 (320 upstream) : MAFA (44806 downstream)																							TCCCCTGCTGCCCCCCCCCCC	0.721													3	3	---	---	---	---	
ARHGAP39	80728	broad.mit.edu	37	8	145816485	145816485	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145816485delC	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	NM_025251	NP_079527	Q9C0H5	RHG39_HUMAN	KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0						ACCTTTGCTTCCATGACCTCC	0.652													4	2	---	---	---	---	
ZNF7	7553	broad.mit.edu	37	8	146051347	146051347	+	5'Flank	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146051347delG	uc003zeg.3	+						ZNF7_uc010mge.2_5'Flank|ZNF7_uc011lln.1_5'Flank|ZNF7_uc003zeh.2_5'Flank	NM_003416	NP_003407	P17097	ZNF7_HUMAN	zinc finger protein 7						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		agaaagaaaagggggaactgg	0.229													4	2	---	---	---	---	
KANK1	23189	broad.mit.edu	37	9	497716	497716	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:497716delG	uc003zgl.1	+							NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a						negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		agccaggcgtggtggcgtgtg	0.000													4	2	---	---	---	---	
GLIS3	169792	broad.mit.edu	37	9	4280511	4280511	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4280511delA	uc003zhx.1	-						GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron	NM_001042413	NP_001035878	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform a						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GGCAAAATGCAAAAAAAAGTT	0.199													4	2	---	---	---	---	
GLDC	2731	broad.mit.edu	37	9	6556087	6556087	+	Intron	DEL	T	-	-	rs113823772		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6556087delT	uc003zkc.2	-							NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	GAAGTCAGAATTTTTTTTTTT	0.428													5	3	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	7103596	7103596	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7103596delC	uc003zkh.2	+						KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						TTTTTTTTTTCTTCTCTAGTA	0.383													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	21114201	21114202	+	IGR	DEL	CA	-	-	rs144198147	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21114201_21114202delCA								IFNB1 (36258 upstream) : IFNW1 (26429 downstream)																							tgcacacatgcacacacacaca	0.287													4	2	---	---	---	---	
UBAP2	55833	broad.mit.edu	37	9	33940059	33940061	+	Intron	DEL	AAG	-	-	rs147216266		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33940059_33940061delAAG	uc003ztq.1	-						UBAP2_uc011loc.1_Intron|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_Intron|UBAP2_uc011lof.1_Intron|UBAP2_uc011log.1_Intron|UBAP2_uc003ztr.2_Intron|UBAP2_uc003zts.2_Intron	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2											ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		ggagaggggAaagaagaagaaaa	0.133													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66478281	66478281	+	IGR	DEL	A	-	-	rs58222709		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66478281delA								FAM74A4 (983895 upstream) : LOC442421 (18189 downstream)																							ttatttttttattatacttta	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66486940	66486940	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66486940delA								FAM74A4 (992554 upstream) : LOC442421 (9530 downstream)																							CCCGCCCCCCAATACCTGCCC	0.731													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66695553	66695553	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66695553delC	uc004aej.2	-											Homo sapiens cDNA clone IMAGE:4668947, partial cds.																		gttgagcaaacagggaaggaa	0.015													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66990579	66990579	+	IGR	DEL	T	-	-	rs140894478	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66990579delT								LOC442421 (487552 upstream) : AQP7P1 (263688 downstream)																							tgctcaatcataagaaatttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68352138	68352138	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68352138delG								FAM27B (557949 upstream) : MIR1299 (650101 downstream)																							tgctatagccgcctaactggt	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68479214	68479214	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68479214delA								FAM27B (685025 upstream) : MIR1299 (523025 downstream)																							aggagggaataaaaaaagagg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68481999	68482001	+	IGR	DEL	TTT	-	-	rs80263272		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68481999_68482001delTTT								FAM27B (687810 upstream) : MIR1299 (520238 downstream)																							ggggaaaatgttttaaaccatat	0.000													4	2	---	---	---	---	
PGM5	5239	broad.mit.edu	37	9	71071663	71071663	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71071663delC	uc004agr.2	+							NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2						gcctcaacctcccaagtagct	0.000													4	2	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72745994	72745994	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72745994delT	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						gatcaaagtattggcagatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81651253	81651253	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81651253delT								PSAT1 (706246 upstream) : TLE4 (535625 downstream)																							tacaCTAGACTTTTTTTTTTT	0.264													5	3	---	---	---	---	
TLE4	7091	broad.mit.edu	37	9	82269146	82269146	+	Intron	DEL	T	-	-	rs35639126		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82269146delT	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5						GTGTGGTTGattttttttttt	0.303													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85818556	85818556	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85818556delA								RASEF (140513 upstream) : FRMD3 (39349 downstream)																							gaaaataggtaagtagaccag	0.040													4	2	---	---	---	---	
AGTPBP1	23287	broad.mit.edu	37	9	88286032	88286032	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88286032delT	uc011ltd.1	-						AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7						aattttttccttttttttttt	0.000													4	2	---	---	---	---	
DAPK1	1612	broad.mit.edu	37	9	90113865	90113866	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90113865_90113866insT	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_5'Flank|DAPK1_uc011lth.1_5'Flank	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						TTATTATTGCCTTTTTTTTTTC	0.564									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				4	2	---	---	---	---	
NXNL2	158046	broad.mit.edu	37	9	91161064	91161065	+	Intron	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91161064_91161065delGT	uc004aqa.2	+							NM_145283	NP_660326	Q5VZ03	NXNL2_HUMAN	nucleoredoxin-like 2 isoform 2												0						CTGAGTGTTCgtgtgtgtgtgt	0.307													4	2	---	---	---	---	
ABCA1	19	broad.mit.edu	37	9	107640614	107640614	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107640614delG	uc004bcl.2	-						ABCA1_uc004bcm.2_Intron	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	AAAAGTGGGTGAGGCACCCTG	0.378													4	2	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112640951	112640951	+	Intron	DEL	C	-	-	rs138796719		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112640951delC	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						caccagatgacccctggactt	0.000													4	2	---	---	---	---	
SVEP1	79987	broad.mit.edu	37	9	113129762	113129762	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113129762delA	uc010mtz.2	-						SVEP1_uc010mty.2_Intron	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						TACAAACTTTAAGGCATTCAG	0.224													4	2	---	---	---	---	
SVEP1	79987	broad.mit.edu	37	9	113192388	113192389	+	Intron	DEL	TT	-	-	rs11331398		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113192388_113192389delTT	uc010mtz.2	-						SVEP1_uc010mty.2_5'Flank	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						gtttgttttctttttttttttt	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120239514	120239515	+	IGR	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120239514_120239515insA								ASTN2 (62197 upstream) : TLR4 (226945 downstream)																							cagtctccaagaaaaaaaaaat	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122806412	122806413	+	IGR	DEL	CA	-	-	rs113767699		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122806412_122806413delCA								DBC1 (674673 upstream) : MIR147 (200844 downstream)																							CCCTCTCTCTcacacacacaca	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123707359	123707360	+	IGR	DEL	AC	-	-	rs34347786		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123707359_123707360delAC								TRAF1 (15880 upstream) : C5 (7256 downstream)																							TCCAACACCAacacacacacac	0.386													4	2	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123846825	123846825	+	Intron	DEL	T	-	-	rs67977982		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123846825delT	uc004bkw.2	+									Q7Z7A1	CNTRL_HUMAN	SubName: Full=Centrosomal protein 110kDa;						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						GAGGATGTCAttttttttttt	0.169													4	2	---	---	---	---	
DAB2IP	153090	broad.mit.edu	37	9	124377911	124377911	+	Intron	DEL	T	-	-	rs10710830		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124377911delT	uc004bln.2	+							NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2						ACtttctttcttttttttttt	0.234													3	3	---	---	---	---	
CCBL1	883	broad.mit.edu	37	9	131598531	131598532	+	Intron	DEL	TC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131598531_131598532delTC	uc004bwh.2	-						CCBL1_uc004bwf.2_Intron|CCBL1_uc004bwg.2_Intron|CCBL1_uc010myn.2_Intron|CCBL1_uc004bwj.2_Intron|CCBL1_uc011mbl.1_Intron|CCBL1_uc004bwi.2_Intron|CCBL1_uc010myo.2_Intron	NM_004059	NP_004050	Q16773	KAT1_HUMAN	kynurenine aminotransferase I isoform a						kynurenine metabolic process|L-phenylalanine catabolic process|tryptophan catabolic process	cytosol|nucleus	1-aminocyclopropane-1-carboxylate synthase activity|cysteine-S-conjugate beta-lyase activity|glutamine-phenylpyruvate transaminase activity|kynurenine-oxoglutarate transaminase activity|L-glutamine:pyruvate aminotransferase activity|L-phenylalanine:pyruvate aminotransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					L-Glutamine(DB00130)|Pyridoxal Phosphate(DB00114)	cttccttctttctctctctctc	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132415669	132415672	+	IGR	DEL	AAAC	-	-	rs34077214		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132415669_132415672delAAAC								ASB6 (11225 upstream) : PRRX2 (12248 downstream)																							ctgtctcaaaaaacaaacaaacaa	0.132													3	4	---	---	---	---	
NCS1	23413	broad.mit.edu	37	9	132971156	132971157	+	Intron	DEL	TG	-	-	rs35560339		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132971156_132971157delTG	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101	P62166	NCS1_HUMAN	frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0						cacacagctctgtgtgtgtgtg	0.262													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3243820	3243820	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3243820delG								PITRM1 (28817 upstream) : KLF6 (574369 downstream)																							caCTTCCCTAGTGTGAATGTG	0.333													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	5664129	5664144	+	IGR	DEL	CACAGGACCCTGTCAT	-	-	rs139668609		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5664129_5664144delCACAGGACCCTGTCAT								CALML3 (95904 upstream) : ASB13 (16676 downstream)																							gtctctgtggcacaggaccctgtcatcatgccagca	0.000													4	2	---	---	---	---	
PLXDC2	84898	broad.mit.edu	37	10	20504185	20504189	+	Intron	DEL	CATGG	-	-	rs56177372		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20504185_20504189delCATGG	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						agtaggacaccatggaagatgttgg	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39084527	39084528	+	IGR	INS	-	C	C			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39084527_39084528insC								LOC399744 (343447 upstream) : None (None downstream)																							tccattcgagtaaatcctttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42364867	42364871	+	IGR	DEL	TTTAA	-	-	rs138889455	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42364867_42364871delTTTAA								None (None upstream) : LOC441666 (462444 downstream)																							tccattccattttaatccattccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42632398	42632399	+	IGR	INS	-	C	C	rs61845554	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42632398_42632399insC								None (None upstream) : LOC441666 (194916 downstream)																							TTCTCTTCTATTACACATTCCA	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42676291	42676292	+	IGR	DEL	AG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42676291_42676292delAG								None (None upstream) : LOC441666 (151023 downstream)																							acacagagacagagattgcagt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42700107	42700108	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42700107_42700108insT								None (None upstream) : LOC441666 (127207 downstream)																							atgtgcttacgtatcatccatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42815103	42815104	+	IGR	INS	-	AACTG	AACTG			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42815103_42815104insAACTG								None (None upstream) : LOC441666 (12211 downstream)																							cattccaatccattccattcca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44393288	44393291	+	IGR	DEL	CTCT	-	-	rs34392993		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44393288_44393291delCTCT								HNRNPA3P1 (107423 upstream) : CXCL12 (472316 downstream)																							tctccctaaactctctctgtgttg	0.000													3	3	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47018723	47018728	+	Intron	DEL	AAAACA	-	-	rs71223641		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47018723_47018728delAAAACA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						aaaacaaaacaaaacaaaaaaacaac	0.000													5	3	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47106937	47106938	+	Intron	INS	-	A	A	rs140415031		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47106937_47106938insA	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						TACTCAGAAGGAAAGGCATGTG	0.455													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	55116634	55116635	+	IGR	DEL	TG	-	-	rs112327655		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55116634_55116635delTG								MBL2 (585174 upstream) : PCDH15 (445900 downstream)																							acaCCTAATTtgtgtgtgtgtg	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	60157510	60157511	+	IGR	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60157510_60157511delTG								TFAM (1614 upstream) : BICC1 (115393 downstream)																							AAGTCTTATTtgtgtgtgtgtg	0.153													4	2	---	---	---	---	
CCDC6	8030	broad.mit.edu	37	10	61616187	61616187	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61616187delA	uc001jks.3	-							NM_005436	NP_005427	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6							cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton			ovary(3)|breast(1)	4				Kidney(211;0.0597)		CATGCATCATAAAAAAAGTAT	0.358													4	2	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	62117858	62117861	+	Intron	DEL	ACAC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62117858_62117861delACAC	uc001jky.2	-						ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						gcatatgtatacacacacacacac	0.000													4	2	---	---	---	---	
JMJD1C	221037	broad.mit.edu	37	10	64984822	64984822	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64984822delA	uc001jmn.2	-						JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Intron|JMJD1C_uc010qiq.1_Intron|JMJD1C_uc009xpi.2_Intron|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc001jmp.1_Intron	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					ctctgtctcgaaaaaaaaaga	0.129													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68120687	68120688	+	Intron	INS	-	TC	TC	rs139544295	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68120687_68120688insTC	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						cttcctttctgtctctctctct	0.000													3	3	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68417994	68417995	+	Intron	INS	-	TCTA	TCTA			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68417994_68417995insTCTA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						ttctctctctctctctctcccc	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	71403205	71403206	+	IGR	INS	-	A	A	rs142037545	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71403205_71403206insA								C10orf35 (9858 upstream) : COL13A1 (158438 downstream)																							cccaccaggtgagaagctccat	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	72042888	72042889	+	IGR	INS	-	TG	TG	rs113088368		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72042888_72042889insTG								NPFFR1 (16740 upstream) : LRRC20 (15840 downstream)																							CTCTCTCTTTTtgtgtgtgtgt	0.361													6	3	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76378771	76378772	+	Intron	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76378771_76378772delTG	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	ttatgctctttgtgtgtgtgtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	76524102	76524102	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76524102delG								ADK (55043 upstream) : MYST4 (62277 downstream)																							GGCGACACCAGTTGAAACAGG	0.552													3	4	---	---	---	---	
ZMIZ1	57178	broad.mit.edu	37	10	80904275	80904275	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80904275delC	uc001kaf.2	+						ZMIZ1_uc001kae.2_Intron	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			tgtgtccccACCCCACCCCAC	0.323													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	83933431	83933446	+	Intron	DEL	ACACACACACACACAC	-	-	rs72353868		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83933431_83933446delACACACACACACACAC	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GCATATGTGAacacacacacacacacacacacacac	0.370													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	84868842	84868842	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84868842delG								NRG3 (121907 upstream) : None (None downstream)																							ctctcctgctggctgagtgca	0.000													3	4	---	---	---	---	
GRID1	2894	broad.mit.edu	37	10	87408593	87408593	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87408593delG	uc001kdl.1	-						GRID1_uc009xsu.1_Intron|GRID1_uc010qmf.1_Intron	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	GGGCTTCTATGGCAGCATGAG	0.368										Multiple Myeloma(13;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	116563017	116563017	+	IGR	DEL	A	-	-	rs79130340		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116563017delA								ABLIM1 (34998 upstream) : FAM160B1 (18486 downstream)																							actctgtctcaaaaaaaaaaa	0.030													4	2	---	---	---	---	
EMX2OS	196047	broad.mit.edu	37	10	119269535	119269535	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119269535delT	uc001ldf.2	-						EMX2OS_uc001ldg.2_Intron					Homo sapiens cDNA FLJ41539 fis, clone BRTHA2018165.												0						GTGCTCATGGTTCATTTGttc	0.264													4	2	---	---	---	---	
HTRA1	5654	broad.mit.edu	37	10	124227291	124227291	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124227291delA	uc001lgj.2	+							NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor						proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				CTCTGCCGTTAAAAAAAAAAG	0.443													3	3	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127697233	127697234	+	Intron	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127697233_127697234delTG	uc001ljh.3	+						FANK1_uc009yan.2_Intron|FANK1_uc001lji.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TGGGTTTGACTGTGTGTGTGTG	0.426													4	3	---	---	---	---	
ADAM12	8038	broad.mit.edu	37	10	127862800	127862801	+	Intron	DEL	AG	-	-	rs1676754	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127862800_127862801delAG	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		ACAAacacacagagtgtttttg	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132677430	132677431	+	IGR	INS	-	AGG	AGG	rs146163825	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132677430_132677431insAGG								GLRX3 (694646 upstream) : TCERG1L (213225 downstream)																							AAGGGAGTGGAAGGAGGACGCG	0.386													3	3	---	---	---	---	
STK32C	282974	broad.mit.edu	37	10	134080953	134080953	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134080953delG	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.1_Intron	NM_173575	NP_775846	Q86UX6	ST32C_HUMAN	serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		cagtgcgtgtgcatgcatgtg	0.065													4	2	---	---	---	---	
INPP5A	3632	broad.mit.edu	37	10	134439345	134439350	+	Intron	DEL	TGTGTG	-	-	rs112908742		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134439345_134439350delTGTGTG	uc001llp.2	+						INPP5A_uc001llo.1_Intron|INPP5A_uc001llq.2_Intron	NM_005539	NP_005530	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase A						cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		GCAGGACTTCtgtgtgtgtgtgtgtg	0.311													2	4	---	---	---	---	
STIM1	6786	broad.mit.edu	37	11	3955451	3955451	+	Intron	DEL	T	-	-	rs112601248		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3955451delT	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		TTCAGCACTCTTTTTTTTTTT	0.438													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	7711940	7711940	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7711940delT								CYB5R2 (16946 upstream) : OVCH2 (505 downstream)																							caaggcaatattttgccttct	0.000													4	2	---	---	---	---	
SPON1	10418	broad.mit.edu	37	11	14165239	14165239	+	Intron	DEL	A	-	-	rs35865034		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14165239delA	uc001mle.2	+							NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		GCAGGATTTCAGTCCTGTAGA	0.483													2	6	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16218185	16218185	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16218185delC	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						CTCTCCTCTTCCATACTCACT	0.388													6	3	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	16896900	16896901	+	Intron	INS	-	T	T	rs59381740		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16896900_16896901insT	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						AGAATACTAAATTTTTTTTTTT	0.149													4	2	---	---	---	---	
DBX1	120237	broad.mit.edu	37	11	20180396	20180396	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20180396delG	uc001mpw.1	-							NM_001029865	NP_001025036	A6NMT0	DBX1_HUMAN	developing brain homeobox 1						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AAACCTTTGTGGGGAATCGTG	0.617													4	2	---	---	---	---	
EHF	26298	broad.mit.edu	37	11	34644849	34644849	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34644849delT	uc001mvr.1	+						EHF_uc009yke.1_Intron|EHF_uc009ykf.1_Intron	NM_012153	NP_036285	Q9NZC4	EHF_HUMAN	ets homologous factor						cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			gccaggctggttttgaactcc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48353007	48353010	+	IGR	DEL	AGTC	-	-	rs150547515		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48353007_48353010delAGTC								OR4C3 (5527 upstream) : OR4C45 (13892 downstream)																							AGTCAGAGTTAGTCAGGAACAAAA	0.235													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50697627	50697627	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50697627delA								LOC646813 (317824 upstream) : OR4A5 (713821 downstream)																							gaattctgagaaaatttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50699243	50699243	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50699243delG								LOC646813 (319440 upstream) : OR4A5 (712205 downstream)																							caccctttttgtagaatctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50748777	50748777	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50748777delA								LOC646813 (368974 upstream) : OR4A5 (662671 downstream)																							cacacatcacaaaaaagtttc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56196964	56196964	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56196964delT								OR5R1 (11256 upstream) : OR5M9 (32983 downstream)																							gcttcaaaagttgaacgaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56249399	56249402	+	IGR	DEL	AAGG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56249399_56249402delAAGG								OR5M3 (11426 upstream) : OR5M8 (8509 downstream)																							gaaacaaagaaaggaaggaaggaa	0.000													3	4	---	---	---	---	
SLC22A8	9376	broad.mit.edu	37	11	62768726	62768727	+	Intron	DEL	TC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62768726_62768727delTC	uc001nwo.2	-						SLC22A8_uc001nwn.1_5'Flank|SLC22A8_uc001nwp.2_Intron|SLC22A8_uc009yom.2_Intron|SLC22A8_uc010rmm.1_Intron|SLC22A8_uc009yon.2_Intron	NM_004254	NP_004245	Q8TCC7	S22A8_HUMAN	solute carrier family 22 member 8						response to toxin	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|organic anion transmembrane transporter activity			skin(2)|ovary(1)	3						gcagatccagtctctctctctc	0.020													4	5	---	---	---	---	
FLRT1	23769	broad.mit.edu	37	11	63881343	63881344	+	Intron	INS	-	ATGG	ATGG			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63881343_63881344insATGG	uc001nyi.1	+						MACROD1_uc001nyh.2_Intron	NM_013280	NP_037412	Q9NZU1	FLRT1_HUMAN	fibronectin leucine rich transmembrane protein						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity				0						tggattgatacatggatggatg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	67506013	67506013	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67506013delA								ALDH3B2 (57328 upstream) : LOC645332 (53227 downstream)																							CGAGAGCTGTAAGGAAAGCCA	0.483													4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70534817	70534817	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70534817delA	uc001oqc.2	-							NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			agaggctgggagggaacacgg	0.129													4	2	---	---	---	---	
POLD3	10714	broad.mit.edu	37	11	74313654	74313655	+	Intron	INS	-	CCT	CCT	rs138945922	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74313654_74313655insCCT	uc001ovf.1	+						POLD3_uc009yua.1_Intron	NM_006591	NP_006582	Q15054	DPOD3_HUMAN	DNA-directed DNA polymerase delta 3						base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding			kidney(2)|ovary(1)	3	Breast(11;3.21e-06)					tattgcaatagcctaactggtc	0.000													2	4	---	---	---	---	
MOGAT2	80168	broad.mit.edu	37	11	75430011	75430012	+	Intron	INS	-	TC	TC	rs149754751	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75430011_75430012insTC	uc010rru.1	+						MOGAT2_uc001oww.1_Intron|MOGAT2_uc010rrv.1_5'Flank	NM_025098	NP_079374	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2						glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			ovary(2)	2	Ovarian(111;0.103)					CCAtctctctttctctctctct	0.104													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76009880	76009882	+	IGR	DEL	TTT	-	-	rs113425683		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76009880_76009882delTTT								WNT11 (88077 upstream) : PRKRIR (51122 downstream)																							tctttctttcttttttttttttt	0.232													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76385631	76385631	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76385631delG								LRRC32 (3840 upstream) : GUCY2E (5580 downstream)																							ACCCCCTCATGGCAGCACTTA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76437289	76437290	+	IGR	INS	-	CTT	CTT	rs142653999	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76437289_76437290insCTT								GUCY2E (4456 upstream) : TSKU (56995 downstream)																							caagccaggtgcttctgggcaa	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	80655407	80655408	+	IGR	INS	-	T	T	rs142315766	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80655407_80655408insT								None (None upstream) : None (None downstream)																							CTTGCATCAGCTGAGCTTTTGG	0.272													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81370100	81370100	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81370100delG								None (None upstream) : None (None downstream)																							TGACCTCTTTGGCCCACATGC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81565871	81565871	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81565871delA								None (None upstream) : FAM181B (877182 downstream)																							agactaactcaaaagggcatg	0.015													4	2	---	---	---	---	
PRCP	5547	broad.mit.edu	37	11	82536662	82536665	+	Intron	DEL	GGGG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82536662_82536665delGGGG	uc001ozs.2	-						PRCP_uc001ozr.2_Intron	NM_005040	NP_005031	P42785	PCP_HUMAN	prolylcarboxypeptidase isoform 1 preproprotein						blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity			skin(1)	1						gagggaagaagggggaaagggagg	0.103													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	86411805	86411805	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86411805delA								ME3 (28127 upstream) : PRSS23 (99686 downstream)																							AGACTTCAATAAAAATATACG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87118256	87118256	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87118256delT								TMEM135 (83688 upstream) : RAB38 (728175 downstream)																							agatctggtattgcaagctgt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93351147	93351148	+	IGR	INS	-	T	T	rs147550240	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93351147_93351148insT								C11orf75 (74601 upstream) : KIAA1731 (43668 downstream)																							ctccatggccactttcgatcat	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	95353041	95353041	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95353041delC								SESN3 (387336 upstream) : FAM76B (149065 downstream)																							gataacactacagaaaaccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	97973156	97973156	+	IGR	DEL	A	-	-	rs140736494		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97973156delA								None (None upstream) : CNTN5 (918715 downstream)																							ctcaagtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102634356	102634356	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102634356delC								MMP8 (38671 upstream) : MMP10 (6878 downstream)																							CCTCCTCCCTCCACTGATTCA	0.438													4	2	---	---	---	---	
PDGFD	80310	broad.mit.edu	37	11	104005610	104005610	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104005610delT	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		TATTCTCAGCTTAGCTTTCAT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107762594	107762594	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107762594delT								SLC35F2 (32680 upstream) : RAB39 (36683 downstream)																							accctgttcattttttttttc	0.100													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110913848	110913848	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110913848delA								ARHGAP20 (329936 upstream) : C11orf53 (212859 downstream)																							agactctgtcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110968059	110968060	+	IGR	INS	-	CCC	CCC	rs139875458	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110968059_110968060insCCC								ARHGAP20 (384147 upstream) : C11orf53 (158647 downstream)																							acttctggaggccccaccccgt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115660674	115660675	+	IGR	DEL	TG	-	-	rs111354654		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115660674_115660675delTG								CADM1 (285433 upstream) : BUD13 (958213 downstream)																							ctttacaaattgtgtgtgtgtg	0.144													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118293268	118293269	+	IGR	INS	-	TG	TG			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118293268_118293269insTG								ATP5L (12707 upstream) : MLL (13936 downstream)																							taatttttgtttttttttgttt	0.000													4	3	---	---	---	---	
IFT46	56912	broad.mit.edu	37	11	118424154	118424155	+	Intron	INS	-	A	A	rs34453997		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118424154_118424155insA	uc001ptp.1	-						IFT46_uc001pto.1_Intron|IFT46_uc009zaf.1_Intron	NM_020153	NP_064538	Q9NQC8	IFT46_HUMAN	IFT46						flagellum assembly|intraflagellar transport|protein stabilization	microtubule basal body|microtubule-based flagellum|nucleus	protein C-terminus binding				0						aaaactgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118743744	118743744	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118743744delG								DDX6 (81772 upstream) : CXCR5 (10797 downstream)																							agaactagctggggttcctca	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121525177	121525178	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121525177_121525178insT								SORL1 (20706 upstream) : LOC399959 (434633 downstream)																							TGCGTGTAAAGGGAGGCACTGT	0.500											OREG0021432	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	122470497	122470497	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122470497delC								LOC399959 (232030 upstream) : UBASH3B (55901 downstream)																							CCCTAAGTTTCCCCCCATGAC	0.443													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	122518224	122518224	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122518224delG								LOC399959 (279757 upstream) : UBASH3B (8174 downstream)																							GCTATGGGGTGGAAGAAAATT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124029642	124029642	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124029642delT								VWA5A (12026 upstream) : OR8G2 (65756 downstream)																							CCCAATGAGGTGGACTATTAT	0.517													16	10	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126752203	126752203	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126752203delT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		CATTTTAGAATTTTACCTTGC	0.408													4	2	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126875826	126875826	+	5'Flank	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126875826delG	uc001qed.3	-						uc001qef.1_RNA			Q8IZU9	KIRR3_HUMAN	Homo sapiens mRNA for KIAA1867 protein, partial cds.						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		tacccaggtaggcagtaggct	0.169													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128552667	128552668	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128552667_128552668delAC	uc001qek.2	-											Homo sapiens cDNA FLJ35701 fis, clone SPLEN2020007.																		GGGAAATAGGacacacacacac	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128803369	128803370	+	IGR	INS	-	C	C	rs147664986	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128803369_128803370insC								KCNJ5 (15420 upstream) : TP53AIP1 (1902 downstream)																							CTCTGCAATGTCCCCCCTACAC	0.554													4	2	---	---	---	---	
ARHGAP32	9743	broad.mit.edu	37	11	128973320	128973321	+	Intron	DEL	AT	-	-	rs147386567		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128973320_128973321delAT	uc009zcp.2	-						ARHGAP32_uc009zcq.1_Intron	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5						tgtcaaacacatataaccatag	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129500084	129500084	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129500084delA								BARX2 (177911 upstream) : TMEM45B (185657 downstream)																							AATGTTCCATAAGGggccagg	0.204													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	132009561	132009561	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132009561delC	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CACACAGTGACCAGGTGTTGG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133746051	133746052	+	IGR	DEL	GT	-	-	rs35467165		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133746051_133746052delGT								SPATA19 (30659 upstream) : LOC283174 (20278 downstream)																							ctacttttaagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	613616	613616	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:613616delC	uc001qii.1	+							NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CCCGCAGCCGCCCCCCCGCCC	0.299													1	5	---	---	---	---	
RAD52	5893	broad.mit.edu	37	12	1049241	1049241	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1049241delA	uc001qis.1	-						RAD52_uc001qit.1_Intron|RAD52_uc010sdt.1_Intron|RAD52_uc001qiu.1_Intron|RAD52_uc001qiv.1_Intron|RAD52_uc001qiw.1_Intron|RAD52_uc010sdu.1_Intron	NM_134424	NP_602296	P43351	RAD52_HUMAN	RAD52 homolog						DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			actctgtctcaaaaaaaaaaa	0.000								Homologous_recombination					4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4172679	4172680	+	IGR	DEL	CA	-	-	rs139672851	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4172679_4172680delCA								PARP11 (190071 upstream) : CCND2 (210222 downstream)																							acccattgcccacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5141557	5141557	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5141557delT								KCNA1 (114137 upstream) : KCNA5 (11528 downstream)																							ctttcccttcttTTTTTTTTT	0.174													6	3	---	---	---	---	
SLC2A3	6515	broad.mit.edu	37	12	8077568	8077568	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8077568delT	uc001qtr.2	-							NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		ttgtccatgcttcaatcatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	9205804	9205804	+	IGR	DEL	G	-	-	rs144700320		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9205804delG								KLRG1 (42466 upstream) : LOC144571 (11969 downstream)																							tgcctgcgacggggtgtcctg	0.000													2	4	---	---	---	---	
STYK1	55359	broad.mit.edu	37	12	10828826	10828826	+	5'Flank	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10828826delG	uc001qys.2	-							NM_018423	NP_060893	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1							integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8						GCAGTTGTGAGGAAGGAATCT	0.408										HNSCC(73;0.22)			4	2	---	---	---	---	
GPRC5D	55507	broad.mit.edu	37	12	13097780	13097781	+	Intron	INS	-	T	T	rs138260461	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13097780_13097781insT	uc010shp.1	-							NM_018654	NP_061124	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, family C, group 5,							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		tccttccttccttccttctttc	0.000													5	3	---	---	---	---	
GPRC5D	55507	broad.mit.edu	37	12	13099218	13099219	+	Intron	INS	-	T	T	rs112470675		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13099218_13099219insT	uc010shp.1	-							NM_018654	NP_061124	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, family C, group 5,							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		tccttccttccttcctttcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	14434213	14434213	+	IGR	DEL	T	-	-	rs113214591		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14434213delT								GRIN2B (301191 upstream) : ATF7IP (84398 downstream)																							tttcttcttcttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	20916363	20916363	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20916363delT								SLCO1C1 (10045 upstream) : SLCO1B3 (47275 downstream)																							tgctctttgctccatgagaaa	0.000													4	2	---	---	---	---	
BCAT1	586	broad.mit.edu	37	12	25078515	25078515	+	Intron	DEL	T	-	-	rs138428612		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25078515delT	uc001rgd.3	-						BCAT1_uc010siy.1_Intron|BCAT1_uc001rge.3_Intron	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic						branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			lung(1)|breast(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)	cccctccccctctccctctcc	0.045													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	33403693	33403693	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33403693delC								PKP2 (353913 upstream) : SYT10 (124655 downstream)																							gtgctcttgaccatttttttg	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38006852	38006852	+	IGR	DEL	T	-	-	rs35175215		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38006852delT								None (None upstream) : ALG10B (703705 downstream)																							gagttgaacatttttttttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38006984	38006984	+	IGR	DEL	C	-	-	rs138910985		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38006984delC								None (None upstream) : ALG10B (703573 downstream)																							ttctcagaaactattttgtga	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38219835	38219835	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38219835delG								None (None upstream) : ALG10B (490722 downstream)																							atctgaaaatggatatttggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	45997227	45997232	+	IGR	DEL	CCTCCT	-	-	rs143488017	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45997227_45997232delCCTCCT								ANO6 (163040 upstream) : LOC400027 (122578 downstream)																							ACACTATTTGcctcctcctcctcctc	0.087													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47114965	47114965	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47114965delA								SLC38A2 (348320 upstream) : SLC38A4 (43579 downstream)																							CCCTCATTGGAAAAAAAAAAT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48053298	48053298	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48053298delT								FAM113B (422857 upstream) : RPAP3 (2418 downstream)																							TATGTGCTCCTTTTCCAATCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48580324	48580325	+	IGR	DEL	GT	-	-	rs58297056		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48580324_48580325delGT								C12orf68 (615 upstream) : OR10AD1 (15797 downstream)																							gtatatgtgcgtgtgtgtgtgt	0.327													4	2	---	---	---	---	
AQP6	363	broad.mit.edu	37	12	50366105	50366106	+	5'Flank	DEL	GC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50366105_50366106delGC	uc001rvr.1	+						AQP6_uc001rvp.1_Intron|AQP6_uc001rvq.1_Intron	NM_001652	NP_001643	Q13520	AQP6_HUMAN	aquaporin 6						excretion|odontogenesis	integral to plasma membrane|transport vesicle membrane	anion channel activity|water channel activity				0						agggagggGAGCGCGGGGGAGG	0.327													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52459319	52459320	+	IGR	INS	-	T	T	rs72519923		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52459319_52459320insT								NR4A1 (6034 upstream) : C12orf44 (4438 downstream)																							GATGGGACTACCAGAGGGGCTG	0.490													3	3	---	---	---	---	
ATF7	11016	broad.mit.edu	37	12	54012836	54012837	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54012836_54012837insA	uc001sdz.2	-						ATF7_uc010sok.1_Intron|ATF7_uc010sol.1_Intron|ATF7_uc001sea.3_Intron|ATF7_uc001seb.3_Intron	NM_006856	NP_006847	P17544	ATF7_HUMAN	activating transcription factor 7 isoform 2						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2						actctgtctccaaaaaaaaaaa	0.109													3	3	---	---	---	---	
ERBB3	2065	broad.mit.edu	37	12	56471832	56471832	+	5'Flank	DEL	A	-	-	rs76460727		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56471832delA	uc001sjh.2	+						ERBB3_uc009zoj.2_5'Flank|ERBB3_uc010sqb.1_5'Flank|ERBB3_uc001sjg.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor						cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			attccgtgtcaaaaaaaaaaa	0.090													5	3	---	---	---	---	
MIP	4284	broad.mit.edu	37	12	56844932	56844932	+	3'UTR	DEL	C	-	-	rs67007101		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56844932delC	uc001slh.2	-	4					TIMELESS_uc001slf.2_5'Flank|TIMELESS_uc001slg.2_5'Flank	NM_012064	NP_036196	P30301	MIP_HUMAN	major intrinsic protein of lens fiber						response to stimulus|visual perception	gap junction|integral to plasma membrane	structural constituent of eye lens			skin(1)	1						AAAAAAAAAACAACCACATAC	0.423													8	4	---	---	---	---	
BAZ2A	11176	broad.mit.edu	37	12	56999208	56999208	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999208delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						TTTTATGTAAttttttttttt	0.174													4	2	---	---	---	---	
PPM1H	57460	broad.mit.edu	37	12	63111232	63111235	+	Intron	DEL	AGAG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63111232_63111235delAGAG	uc001srk.3	-							NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		ATGCTAATGCagagagagagagag	0.289													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65904944	65904949	+	IGR	DEL	TCCTCC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65904944_65904949delTCCTCC								MSRB3 (44264 upstream) : RPSAP52 (246854 downstream)																							CCACCCCCTTtcctcctcctcctcct	0.374													4	2	---	---	---	---	
HMGA2	8091	broad.mit.edu	37	12	66325331	66325332	+	Intron	INS	-	TG	TG			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66325331_66325332insTG	uc001ssx.2	+						HMGA2_uc001ssw.1_Intron	NM_003483	NP_003474	P52926	HMGA2_HUMAN	high mobility group AT-hook 2 isoform a						cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/RAD51B(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(22)	208	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		TTATAGAtgtttgtgtgtgtgt	0.238			T	 LHFP|RAD51L1|LPP|HEI10|COX6C|CMKOR1|NFIB|ALDH2|CCNB1IP1|EBF1|WIF1|FHIT	lipoma|leiomyoma|pleiomorphic salivary gland adenoma								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68766735	68766735	+	IGR	DEL	G	-	-	rs10709226		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68766735delG								MDM1 (40574 upstream) : RAP1B (237917 downstream)																							GTCAGGAAAAGTTTTTTAGGG	0.363													4	3	---	---	---	---	
TSPAN8	7103	broad.mit.edu	37	12	71812300	71812301	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71812300_71812301insA	uc001swk.1	-							NM_004616	NP_004607	P19075	TSN8_HUMAN	transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)			gaccttgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76620214	76620214	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76620214delA								NAP1L1 (141476 upstream) : BBS10 (118052 downstream)																							gaccctgtctaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	79224987	79224988	+	IGR	INS	-	A	A	rs80080225		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79224987_79224988insA								NAV3 (618199 upstream) : SYT1 (32785 downstream)																							gtcaaaaaaagaaaaaaaaaaa	0.040													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80346031	80346031	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80346031delA								PPP1R12A (16796 upstream) : PTPRQ (492095 downstream)																							gcatccttacaaaagggttgc	0.000													4	2	---	---	---	---	
C12orf26	84190	broad.mit.edu	37	12	82841377	82841377	+	Intron	DEL	C	-	-	rs62934062		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82841377delC	uc001szq.2	+							NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190												0						gtaaggtaaacacaagattca	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	83543293	83543294	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83543293_83543294insT								TMTC2 (15230 upstream) : None (None downstream)																							tattttttttcttttttttgga	0.173													4	2	---	---	---	---	
UBE2N	7334	broad.mit.edu	37	12	93820647	93820647	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93820647delT	uc001tcp.2	-							NM_003348	NP_003339	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N						DNA double-strand break processing|double-strand break repair via homologous recombination|histone ubiquitination|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of DNA repair|positive regulation of histone modification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity|postreplication repair|protein K63-linked ubiquitination|proteolysis|regulation of histone ubiquitination|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-MMS2 complex|UBC13-UEV1A complex|ubiquitin ligase complex	ATP binding|ubiquitin binding|ubiquitin-protein ligase activity				0						CATCAGCAGAttttttttttt	0.264								Direct_reversal_of_damage|Rad6_pathway					4	2	---	---	---	---	
SOCS2	8835	broad.mit.edu	37	12	93968379	93968379	+	Intron	DEL	T	-	-	rs35259505		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93968379delT	uc001tcw.1	+						uc001tcv.1_5'Flank|uc001tcu.2_5'Flank|SOCS2_uc001tcx.1_Intron|SOCS2_uc009zsu.2_3'UTR|SOCS2_uc001tcy.1_Intron|SOCS2_uc001tcz.2_3'UTR	NM_003877	NP_003868	O14508	SOCS2_HUMAN	suppressor of cytokine signaling-2						anti-apoptosis|growth hormone receptor signaling pathway|JAK-STAT cascade|negative regulation of signal transduction|regulation of cell growth|response to estradiol stimulus	cytoplasm	growth hormone receptor binding|insulin-like growth factor receptor binding|JAK pathway signal transduction adaptor activity|prolactin receptor binding|SH3/SH2 adaptor activity			lung(1)	1						ACACACCACCTTTTTTTTTTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93999513	93999514	+	IGR	INS	-	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93999513_93999514insG								SOCS2 (29535 upstream) : CRADD (71637 downstream)																							GAAAGGGAGCAGGGAAAGGAAA	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97538480	97538480	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97538480delA								NEDD1 (191019 upstream) : RMST (320319 downstream)																							ATGAAAAAGCAAGAAAAGAAG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	98142856	98142857	+	Intron	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98142856_98142857delCA	uc001tfc.1	-						uc001tfd.2_Intron					Homo sapiens cDNA FLJ25775 fis, clone TST06543.																		gttattgtttcacacacagagg	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102238823	102238824	+	IGR	INS	-	T	T	rs148090043		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102238823_102238824insT								GNPTAB (14191 upstream) : DRAM1 (32281 downstream)																							CCCTTCATGGATTTTTTTTTTT	0.396													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110073119	110073121	+	IGR	DEL	CAC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110073119_110073121delCAC								MVK (38049 upstream) : C12orf34 (79069 downstream)																							tcaccaccatcaccaccaccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114231068	114231069	+	IGR	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114231068_114231069delCA								LHX5 (321191 upstream) : RBM19 (23474 downstream)																							tgcaaacacgcacacacacaca	0.277													4	2	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116675969	116675969	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116675969delA	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TTAATTAGGGAAGCAGTTAGC	0.289													4	2	---	---	---	---	
RNFT2	84900	broad.mit.edu	37	12	117178463	117178463	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117178463delT	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		gggttactgatttgtctaggg	0.060													2	6	---	---	---	---	
TAOK3	51347	broad.mit.edu	37	12	118647522	118647523	+	Intron	INS	-	T	T	rs149685098		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118647522_118647523insT	uc001twx.2	-						TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					tcttcttcttcttttttttttt	0.010													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	120856299	120856300	+	IGR	DEL	AC	-	-	rs63118660		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120856299_120856300delAC								MSI1 (49341 upstream) : COX6A1 (19604 downstream)																							AGTCTTCAAAACACACACACAC	0.366													4	2	---	---	---	---	
CAMKK2	10645	broad.mit.edu	37	12	121691465	121691465	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121691465delA	uc001tzu.2	-						CAMKK2_uc001tzt.2_Intron|CAMKK2_uc001tzv.2_Intron|CAMKK2_uc001tzw.2_Intron|CAMKK2_uc001tzx.2_Intron|CAMKK2_uc001tzy.2_Intron|CAMKK2_uc001tzz.1_Intron|CAMKK2_uc001uaa.1_Intron|CAMKK2_uc001uab.2_Intron|CAMKK2_uc001uac.2_Intron	NM_006549	NP_006540	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase						calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity	cytoplasm	ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity			lung(1)|large_intestine(1)|stomach(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AGATGAGGGGAAAAGTGTCTT	0.517													4	2	---	---	---	---	
CLIP1	6249	broad.mit.edu	37	12	122848952	122848953	+	Intron	INS	-	T	T	rs35729680		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122848952_122848953insT	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_5'Flank|CLIP1_uc010tae.1_Intron	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TTAGAAAATACttttttttttt	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127142075	127142075	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127142075delA								LOC100128554 (184745 upstream) : None (None downstream)																							TAAATTGTTCAAAGGAAATGC	0.418													4	2	---	---	---	---	
EP400	57634	broad.mit.edu	37	12	132557774	132557774	+	Intron	DEL	T	-	-	rs66669342		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132557774delT	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron|EP400_uc001ujp.2_Intron|EP400_uc010tbo.1_5'Flank	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400						histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		ccaccttctcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132641233	132641234	+	IGR	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132641233_132641234insA								NOC4L (4247 upstream) : GALNT9 (39684 downstream)																							acactacacacaccactacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132912100	132912113	+	IGR	DEL	GTGTGTGCATGCAT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132912100_132912113delGTGTGTGCATGCAT								GALNT9 (6195 upstream) : FBRSL1 (155044 downstream)																							GCATGTACCCgtgtgtgcatgcatgtgtgtgcat	0.037													4	2	---	---	---	---	
TNFRSF19	55504	broad.mit.edu	37	13	24173538	24173538	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24173538delC	uc001uov.1	+						TNFRSF19_uc001uot.2_Intron|TNFRSF19_uc010tcu.1_Intron|TNFRSF19_uc001uow.2_Intron	NM_018647	NP_061117	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		catgacacagccctcgagaga	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30499188	30499189	+	IGR	INS	-	GA	GA	rs142810343	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30499188_30499189insGA								UBL3 (74368 upstream) : KATNAL1 (277579 downstream)																							cgagagcgagcgagagagagag	0.366													4	2	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32868646	32868646	+	Frame_Shift_Del	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32868646delA	uc001utx.2	+	60	9218	c.8722delA	c.(8722-8724)ATGfs	p.M2908fs	FRY_uc010tdw.1_RNA|FRY_uc001utz.2_Frame_Shift_Del_p.M439fs|FRY_uc010tdx.1_Frame_Shift_Del_p.M278fs	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	2908					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CATCCAGTCCATGCTGGAGTG	0.547													39	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	48223047	48223047	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48223047delG								HTR2A (751997 upstream) : SUCLA2 (293745 downstream)																							gtttgaggctggaaagtccaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	48356804	48356804	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48356804delA								HTR2A (885754 upstream) : SUCLA2 (159988 downstream)																							agggtattccaagacctgcag	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63629295	63629296	+	IGR	INS	-	AA	AA	rs142116711	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63629295_63629296insAA								None (None upstream) : OR7E156P (682272 downstream)																							TCTTCCAGCTTAAAAAAATGTG	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64100716	64100727	+	IGR	DEL	ACACACACACAC	-	-	rs72398798		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64100716_64100727delACACACACACAC								None (None upstream) : OR7E156P (210841 downstream)																							acgtccaaatacacacacacacacacacacac	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	65367890	65367891	+	IGR	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65367890_65367891delGT								None (None upstream) : None (None downstream)																							atgaaagagagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68461989	68461990	+	IGR	INS	-	T	T	rs147870249	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68461989_68461990insT								PCDH9 (657521 upstream) : None (None downstream)																							TTGCACTGAAATTTTTGTAATG	0.356													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71669396	71669396	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71669396delA								ATXN8OS (955511 upstream) : DACH1 (342702 downstream)																							cattaaaaggaaaaccttacc	0.000													4	2	---	---	---	---	
KLF12	11278	broad.mit.edu	37	13	74487121	74487122	+	Intron	INS	-	C	C	rs150033060	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74487121_74487122insC	uc001vjf.2	-						KLF12_uc010aeq.2_Intron|KLF12_uc001vjg.3_Intron	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		ctcatgcgttaccttctccaag	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	74832299	74832300	+	IGR	DEL	TG	-	-	rs71118969		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74832299_74832300delTG								KLF12 (123905 upstream) : LOC647288 (979590 downstream)																							TTACtgtgtttgtgtgtgtgtg	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	88270841	88270843	+	Intron	DEL	TGT	-	-	rs34716181		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88270841_88270843delTGT	uc001vlm.1	-											Homo sapiens clone IMAGE:32106, mRNA sequence.																		ATGTCCTCCCtgttgttgttgtt	0.296													3	3	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	93998938	93998938	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93998938delA	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GACAATGAGGAAAGAAGTGAG	0.338													4	2	---	---	---	---	
DOCK9	23348	broad.mit.edu	37	13	99615216	99615217	+	Intron	DEL	AA	-	-	rs141932743		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99615216_99615217delAA	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tis.1_Intron|DOCK9_uc010tit.1_Intron	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GATTGTGAAGAAGAGAGCAGGC	0.554													3	4	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102611373	102611373	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102611373delT	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					tagaccaccctgaaattaccc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104151346	104151346	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104151346delT								SLC10A2 (432150 upstream) : None (None downstream)																							ctctttctccttttttttcct	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105274825	105274826	+	IGR	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105274825_105274826delCA								None (None upstream) : DAOA (843390 downstream)																							AGAAACTGTCcacacacacaca	0.228													4	2	---	---	---	---	
ARHGEF7	8874	broad.mit.edu	37	13	111775842	111775843	+	Intron	DEL	AT	-	-	rs1888846		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111775842_111775843delAT	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ACACACACACATACATGCCCGT	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112767179	112767180	+	IGR	INS	-	C	C	rs142937068	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112767179_112767180insC								SOX1 (41159 upstream) : C13orf28 (263489 downstream)																							caccaccctagccagcacccta	0.272													5	4	---	---	---	---	
MCF2L	23263	broad.mit.edu	37	13	113747897	113747897	+	Intron	DEL	C	-	-	rs34958299		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113747897delC	uc001vsu.2	+						MCF2L_uc001vsq.2_Intron|MCF2L_uc010tjr.1_Intron|MCF2L_uc001vsr.2_Intron|MCF2L_uc010tjs.1_Intron	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CCTCTGTCCTCCCCATGCCCC	0.567											OREG0003846	type=REGULATORY REGION|Gene=MCF2L|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	4	---	---	---	---	
ADPRHL1	113622	broad.mit.edu	37	13	114087762	114087762	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114087762delT	uc001vtq.1	-						ADPRHL1_uc001vtp.1_Intron	NM_138430	NP_612439	Q8NDY3	ARHL1_HUMAN	ADP-ribosylhydrolase like 1 isoform 1						protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)			CTAATCCTGCTTTTGGGCTGA	0.403													4	2	---	---	---	---	
RASA3	22821	broad.mit.edu	37	13	114796752	114796755	+	Intron	DEL	TGTG	-	-	rs149675975		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114796752_114796755delTGTG	uc001vui.2	-						RASA3_uc010tkk.1_Intron|RASA3_uc001vuj.2_Intron|RASA3_uc010tkl.1_Intron|RASA3_uc010aha.1_Intron	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			TGCATGAAACTGtgtgtgtctgcc	0.118													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19816782	19816784	+	IGR	DEL	TGT	-	-	rs113555299		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19816782_19816784delTGT								POTEG (231840 upstream) : P704P (167170 downstream)																							tgagcaatgatgttgagcacttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19818346	19818347	+	IGR	INS	-	TG	TG			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19818346_19818347insTG								POTEG (233404 upstream) : P704P (165607 downstream)																							ttttggttttttttgtttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	29469705	29469705	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29469705delG								C14orf23 (205706 upstream) : PRKD1 (575984 downstream)																							aaaagataaagggagaagaaa	0.000													4	2	---	---	---	---	
FERMT2	10979	broad.mit.edu	37	14	53340667	53340667	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53340667delT	uc001xad.2	-						FERMT2_uc001xac.2_Intron|FERMT2_uc001xae.2_Intron|FERMT2_uc001xaf.2_Intron	NM_006832	NP_006823	Q96AC1	FERM2_HUMAN	fermitin family homolog 2 isoform 1						actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)					TTTCACAATCTTTTTTTTTTT	0.343													3	3	---	---	---	---	
C14orf105	55195	broad.mit.edu	37	14	57949802	57949803	+	Frame_Shift_Ins	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57949802_57949803insT	uc001xcy.2	-	3	516_517	c.373_374insA	c.(373-375)AGGfs	p.R125fs	C14orf105_uc010trl.1_Frame_Shift_Ins_p.R125fs|C14orf105_uc010trm.1_Frame_Shift_Ins_p.R37fs|C14orf105_uc010trn.1_Frame_Shift_Ins_p.R37fs|C14orf105_uc001xcz.2_Frame_Shift_Ins_p.R125fs|C14orf105_uc010aox.1_RNA|C14orf105_uc010aoy.1_Frame_Shift_Ins_p.R47fs	NM_018168	NP_060638	Q9NVL8	CN105_HUMAN	hypothetical protein LOC55195	125											0						GTGCATTGTCCTGGCTTCTCGC	0.530													22	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	59243886	59243887	+	IGR	INS	-	GGT	GGT	rs143337073	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59243886_59243887insGGT								DACT1 (128850 upstream) : DAAM1 (411512 downstream)																							AGGTGGTCACAGGTGGTCACCT	0.277													3	3	---	---	---	---	
DAAM1	23002	broad.mit.edu	37	14	59719595	59719595	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59719595delA	uc001xdz.1	+						DAAM1_uc001xea.1_Intron|DAAM1_uc001xeb.1_Intron|DAAM1_uc001xdy.2_Intron	NM_014992	NP_055807	Q9Y4D1	DAAM1_HUMAN	dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)		TCCCTGGGCTAAGAAGCAATC	0.284													4	2	---	---	---	---	
ACTN1	87	broad.mit.edu	37	14	69354379	69354381	+	Intron	DEL	CTT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69354379_69354381delCTT	uc001xkl.2	-						ACTN1_uc001xkk.2_5'UTR|ACTN1_uc010ttb.1_Intron|ACTN1_uc001xkm.2_Intron|ACTN1_uc001xkn.2_Intron|ACTN1_uc010ttc.1_5'Flank|ACTN1_uc001xko.1_Intron|ACTN1_uc010ttd.1_Intron	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b						focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GGATACCCTCCTTCTTAAAAATG	0.330													2	4	---	---	---	---	
SLC24A4	123041	broad.mit.edu	37	14	92918365	92918365	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92918365delC	uc001yak.2	+						SLC24A4_uc001yai.2_Intron|SLC24A4_uc010twm.1_Intron|SLC24A4_uc001yaj.2_Intron|SLC24A4_uc010auj.2_Intron|SLC24A4_uc010twn.1_Intron|SLC24A4_uc001yan.2_5'Flank|uc001yal.1_5'Flank|uc001yam.1_5'Flank	NM_153646	NP_705932	Q8NFF2	NCKX4_HUMAN	solute carrier family 24 member 4 isoform 1							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		GACAAGCTGTCCCGGGAGGCA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95209472	95209472	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95209472delG								SERPINA13 (96142 upstream) : GSC (25089 downstream)																							ccagcactttgggaggccaag	0.025													4	2	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95711325	95711326	+	Intron	INS	-	AC	AC	rs141507842	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95711325_95711326insAC	uc001yef.2	-							NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		TATATGTGTATacacacacaca	0.050													5	3	---	---	---	---	
VRK1	7443	broad.mit.edu	37	14	97333794	97333795	+	Intron	DEL	GT	-	-	rs72133015		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97333794_97333795delGT	uc001yft.2	+							NM_003384	NP_003375	Q99986	VRK1_HUMAN	vaccinia related kinase 1							cytoplasm|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity			large_intestine(1)|stomach(1)	2		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		ctgtgcacaagtgtgtgtgtgt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97537264	97537265	+	IGR	DEL	TG	-	-	rs71916417		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97537264_97537265delTG								VRK1 (189314 upstream) : C14orf64 (854682 downstream)																							GTGGGGATTTtgtgtgtgtgtg	0.366													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98097638	98097638	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98097638delA								VRK1 (749688 upstream) : C14orf64 (294309 downstream)																							TGGCTCAGTTAAAAAAAAAAA	0.323													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106881532	106881533	+	Intron	INS	-	TAGA	TAGA	rs149406887	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106881532_106881533insTAGA	uc010tyt.1	-						uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0						tgattgacacttagattatttg	0.089													7	6	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107033165	107033165	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107033165delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ggtgatagtgaagcatcttgt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20007655	20007655	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20007655delG								None (None upstream) : GOLGA6L6 (729439 downstream)																							ttctcagattgtttctgtgta	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20019051	20019051	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20019051delC								None (None upstream) : GOLGA6L6 (718043 downstream)																							gaatatatttccttttctaac	0.000													6	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20042672	20042672	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20042672delA								None (None upstream) : GOLGA6L6 (694422 downstream)																							ctgctcaatcaaaacaaagtt	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20427031	20427032	+	IGR	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20427031_20427032delCA								None (None upstream) : GOLGA6L6 (310062 downstream)																							AGACACCTAGCACAGAGTTTAG	0.411													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20437048	20437049	+	IGR	INS	-	ACAC	ACAC	rs113823452		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20437048_20437049insACAC								None (None upstream) : GOLGA6L6 (300045 downstream)																							cccctctctctacacacacaca	0.079													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20445154	20445155	+	IGR	INS	-	AA	AA	rs141413515		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20445154_20445155insAA								None (None upstream) : GOLGA6L6 (291939 downstream)																							tgggtgCAATTAAAAAAAAAAA	0.015													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20561114	20561115	+	IGR	INS	-	TTTC	TTTC	rs144255660	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20561114_20561115insTTTC								None (None upstream) : GOLGA6L6 (175979 downstream)																							GCTTCTTCTCttttctttcttt	0.228													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20601516	20601517	+	Intron	DEL	TG	-	-	rs113700902		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20601516_20601517delTG	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		AAGTGCCACATGTGTTTGCAAA	0.411													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21925811	21925812	+	IGR	INS	-	GT	GT	rs4613029		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21925811_21925812insGT								NF1P1 (791186 upstream) : LOC646214 (6702 downstream)																							cgcgcgcgtgCGCGCGCACGCC	0.366													4	2	---	---	---	---	
TUBGCP5	114791	broad.mit.edu	37	15	22867122	22867123	+	Intron	INS	-	AAG	AAG	rs79823960		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22867122_22867123insAAG	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		AAAAAAAAAAAAAGTTGGTGGT	0.322													6	3	---	---	---	---	
UBE3A	7337	broad.mit.edu	37	15	25595446	25595447	+	Intron	INS	-	A	A	rs34610959		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25595446_25595447insA	uc001zaq.2	-						uc001zae.2_Intron|UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453	Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		tttgtctctttaaaaaaaaaaa	0.183													4	2	---	---	---	---	
GABRG3	2567	broad.mit.edu	37	15	27453473	27453473	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27453473delC	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		AAGTCTGTAGCCCTTTCAAAG	0.507													8	4	---	---	---	---	
APBA2	321	broad.mit.edu	37	15	29142329	29142330	+	Intron	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29142329_29142330delAC	uc010uat.1	+						APBA2_uc010azj.2_Intron|APBA2_uc010uas.1_Intron	NM_001130414	NP_001123886	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		aaaagacacgacacacacacac	0.069													5	3	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29835746	29835747	+	Intron	INS	-	G	G	rs150557726	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29835746_29835747insG	uc010azk.1	-							NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						gcattttgggagctgaggtagg	0.084													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30289678	30289678	+	IGR	DEL	A	-	-	rs112183746		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30289678delA								TJP1 (174972 upstream) : FAM7A3 (106257 downstream)																							tcacgcttccaaaagcaattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	35294202	35294202	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35294202delA								ZNF770 (13748 upstream) : LOC723972 (235325 downstream)																							actccgtctcaaaaaaaaaag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37514575	37514576	+	IGR	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37514575_37514576delTG								MEIS2 (121075 upstream) : TMCO5A (712251 downstream)																							GGGTAGAAAATGTGTGTGTGTG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40373404	40373407	+	IGR	DEL	AAAG	-	-	rs67784152		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40373404_40373407delAAAG								SRP14 (42015 upstream) : BMF (6687 downstream)																							gaaaaaaaaaaaagaagaagaaga	0.343													4	3	---	---	---	---	
INO80	54617	broad.mit.edu	37	15	41323783	41323787	+	Intron	DEL	GGAAG	-	-	rs143682278	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41323783_41323787delGGAAG	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						gaggaagggaggaagggagggaggg	0.063													4	2	---	---	---	---	
NUSAP1	51203	broad.mit.edu	37	15	41665288	41665289	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41665288_41665289insA	uc001zns.3	+						NUSAP1_uc001znq.3_Intron|NUSAP1_uc001znr.3_Intron|NUSAP1_uc010bce.2_Intron|NUSAP1_uc001znt.3_Intron|NUSAP1_uc001znv.3_Intron|NUSAP1_uc001znu.3_Intron|NUSAP1_uc010ucw.1_Intron|NUSAP1_uc001znw.3_Intron	NM_016359	NP_057443	Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		aaccctgtctcaaaaaaaaaaa	0.208													4	2	---	---	---	---	
TTBK2	146057	broad.mit.edu	37	15	43112899	43112899	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43112899delA	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		ctgaagctgcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TUBGCP4	27229	broad.mit.edu	37	15	43693649	43693650	+	Intron	INS	-	A	A	rs79630341		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43693649_43693650insA	uc001zro.2	+						TUBGCP4_uc001zrn.2_Intron|TUBGCP4_uc010bdh.2_Intron	NM_014444	NP_055259	Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	structural constituent of cytoskeleton			ovary(3)	3		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		gactccgtctcaaaaaaaaaaa	0.203													2	5	---	---	---	---	
CEP152	22995	broad.mit.edu	37	15	49077603	49077604	+	Intron	INS	-	CTCAAG	CTCAAG	rs144572205	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49077603_49077604insCTCAAG	uc001zwy.2	-						CEP152_uc001zwz.2_Intron|CEP152_uc001zxa.1_Intron	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa						centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TGCTGCGAATTCCAGGCCAGCT	0.312													2	5	---	---	---	---	
TRPM7	54822	broad.mit.edu	37	15	50855514	50855515	+	Intron	DEL	AT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50855514_50855515delAT	uc001zyt.3	-						TRPM7_uc001zyr.2_Intron	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,						cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TTTATACATCATAGATACAAGC	0.074													4	4	---	---	---	---	
MAPK6	5597	broad.mit.edu	37	15	52349686	52349686	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52349686delC	uc002abp.2	+							NM_002748	NP_002739	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6						cell cycle		ATP binding|MAP kinase activity			lung(3)|ovary(1)	4				all cancers(107;0.0028)		tttctttcttccatatgaatg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63138636	63138636	+	IGR	DEL	T	-	-	rs36010456		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63138636delT								TLN2 (1809 upstream) : TPM1 (196202 downstream)																							tttccaaagcttttttttttt	0.264													4	3	---	---	---	---	
DAPK2	23604	broad.mit.edu	37	15	64296282	64296283	+	Intron	DEL	TC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64296282_64296283delTC	uc002amr.2	-						DAPK2_uc010uim.1_Intron|DAPK2_uc010bgu.1_Intron	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		tttaggttcttctctctctctc	0.000													4	2	---	---	---	---	
IQCH	64799	broad.mit.edu	37	15	67771261	67771261	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67771261delA	uc002aqo.1	+						IQCH_uc002aqq.1_Intron|IQCH_uc002aqp.1_Intron|uc002aqr.1_Intron	NM_001031715	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H isoform 1											skin(3)|ovary(1)	4				Colorectal(3;0.0856)		actctgtctcaaaaaaaaaag	0.134													4	2	---	---	---	---	
MAP2K5	5607	broad.mit.edu	37	15	68078356	68078357	+	Intron	INS	-	T	T	rs11374165		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68078356_68078357insT	uc002aqu.2	+						MAP2K5_uc002aqv.2_Intron|MAP2K5_uc002aqw.2_Intron|MAP2K5_uc002aqx.2_Intron	NM_145160	NP_660143	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2						ctgttaggttgttttttttttt	0.064													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	73931443	73931443	+	IGR	DEL	T	-	-	rs77456216		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73931443delT								NPTN (5690 upstream) : CD276 (45179 downstream)																							tctttctttcttttttttttt	0.154													3	3	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	77138175	77138176	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77138175_77138176insA	uc002bby.2	-						SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron|SCAPER_uc002bcc.1_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						cacagaaacagaaaaaaaatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	77375090	77375091	+	IGR	INS	-	CTCC	CTCC	rs138953087	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77375090_77375091insCTCC								TSPAN3 (11577 upstream) : SGK269 (25380 downstream)																							GAGAGCATCCACTCCCTCCCTC	0.525													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78008623	78008624	+	IGR	DEL	TT	-	-	rs143048795		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78008623_78008624delTT								LINGO1 (20148 upstream) : LOC645752 (197935 downstream)																							cttcttcttctttttttttttt	0.134													4	2	---	---	---	---	
HOMER2	9455	broad.mit.edu	37	15	83607616	83607616	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83607616delT	uc002bjg.2	-						HOMER2_uc002bjh.2_Intron|HOMER2_uc002bjj.2_Intron|HOMER2_uc002bji.2_Intron	NM_199330	NP_955362	Q9NSB8	HOME2_HUMAN	homer 2 isoform 2						metabotropic glutamate receptor signaling pathway	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane					0						gatgctccccttttcagcctc	0.000													6	3	---	---	---	---	
SH3GL3	6457	broad.mit.edu	37	15	84153286	84153286	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84153286delT	uc002bjw.2	+						SH3GL3_uc010bms.2_Intron|SH3GL3_uc010uot.1_Intron|SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3						GTAAAAATAGTTTTTTTTTTC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84851881	84851882	+	IGR	DEL	AC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84851881_84851882delAC								ADAMTSL3 (143290 upstream) : LOC388152 (15718 downstream)																							GTGTGTGTATacacacacacac	0.238													4	3	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87360525	87360525	+	Intron	DEL	A	-	-	rs75525220		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87360525delA	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						ctccatctggaaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87778569	87778570	+	IGR	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87778569_87778570insA								AGBL1 (206286 upstream) : NCRNA00052 (341590 downstream)																							ggctatgccctgccccagaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87857850	87857850	+	IGR	DEL	T	-	-	rs35890536		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87857850delT								AGBL1 (285567 upstream) : NCRNA00052 (262310 downstream)																							AAAAGTCACATTTTTTTTCTA	0.398													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89462618	89462623	+	IGR	DEL	TCTTTC	-	-	rs71149241		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89462618_89462623delTCTTTC								MFGE8 (5955 upstream) : ABHD2 (168758 downstream)																							TCTtttcttttctttctttttttttt	0.175													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90289941	90289942	+	IGR	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90289941_90289942delCA								WDR93 (3073 upstream) : MESP1 (3158 downstream)																							gccccgcctccacacacacaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	91047214	91047214	+	IGR	DEL	A	-	-	rs66813720		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91047214delA								IQGAP1 (1739 upstream) : CRTC3 (25984 downstream)																							actccatctcaaaaaaaaaaa	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	91966788	91966788	+	IGR	DEL	T	-	-	rs35141379		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91966788delT								SV2B (128140 upstream) : SLCO3A1 (430150 downstream)																							TACTTCAGAATGGGCCAAGCT	0.458													4	3	---	---	---	---	
CHD2	1106	broad.mit.edu	37	15	93568101	93568101	+	3'UTR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93568101delG	uc002bsp.2	+	39						NM_001271	NP_001262	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2						regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GCCTTTCACTGGGTCCAGCTC	0.552													4	2	---	---	---	---	
CHD2	1106	broad.mit.edu	37	15	93568466	93568467	+	3'UTR	INS	-	GGG	GGG	rs147197697	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93568466_93568467insGGG	uc002bsp.2	+	39						NM_001271	NP_001262	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2						regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TAGGACTTGAAGGGGAGCAGGT	0.530													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94575613	94575614	+	IGR	INS	-	T	T	rs67833899		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94575613_94575614insT								RGMA (943180 upstream) : MCTP2 (199187 downstream)																							TCTGTAAATAGTTTTTTTTTTT	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95314135	95314136	+	IGR	INS	-	AT	AT	rs140218439		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95314135_95314136insAT								MCTP2 (286955 upstream) : LOC145820 (662186 downstream)																							cacagatacacatacacacaca	0.282													3	5	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6502414	6502430	+	Intron	DEL	CCACGTCTCTCTTCCTG	-	-	rs76033644	byFrequency	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6502414_6502430delCCACGTCTCTCTTCCTG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		tctcttccttccacgtctctcttcctgccatgactcc	0.101													3	4	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6704110	6704113	+	Intron	DEL	TGGA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6704110_6704113delTGGA	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		gctgtttgggtggatggatggatg	0.093													3	3	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7312314	7312315	+	Intron	INS	-	T	T	rs148978014	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7312314_7312315insT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		CCATTTCTCTATTTTTTTTTTC	0.347													3	3	---	---	---	---	
ABAT	18	broad.mit.edu	37	16	8869124	8869125	+	Intron	INS	-	TTTTCCTG	TTTTCCTG	rs141501013	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8869124_8869125insTTTTCCTG	uc002czc.3	+						ABAT_uc002czd.3_Intron|ABAT_uc010buh.2_Intron|ABAT_uc010bui.2_Intron	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	CACCATCAGCCTTTTCCTGTTT	0.391													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13891844	13891845	+	IGR	DEL	AG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13891844_13891845delAG								SHISA9 (557572 upstream) : ERCC4 (122169 downstream)																							aaggaaggaaagagagaaggaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16694985	16694985	+	IGR	DEL	T	-	-	rs113782878		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16694985delT								LOC339047 (250548 upstream) : XYLT1 (501198 downstream)																							atgtctttgcttttttttttt	0.070													3	3	---	---	---	---	
SMG1	23049	broad.mit.edu	37	16	18883764	18883764	+	Intron	DEL	A	-	-	rs117332168	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18883764delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						TCTATCCATTAAAAAAAAAAA	0.313													9	4	---	---	---	---	
METTL9	51108	broad.mit.edu	37	16	21636607	21636607	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21636607delG	uc002dje.2	+						uc002diq.3_Intron|METTL9_uc002djf.2_Intron	NM_016025	NP_057109	Q9H1A3	METL9_HUMAN	methyltransferase like 9 isoform 1											ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0759)		TTCACCTTAAGGTGGACTTTA	0.343													4	2	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22105640	22105641	+	Intron	INS	-	TT	TT			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22105640_22105641insTT	uc010vbq.1	+						VWA3A_uc010bxc.2_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		AGTAAAGCCAGTTTTTTTTTTT	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27027783	27027785	+	IGR	DEL	CCC	-	-	rs10538188		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27027783_27027785delCCC								HS3ST4 (878775 upstream) : C16orf82 (50434 downstream)																							ctttcttcttccccttccccttc	0.015													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27040943	27040944	+	IGR	INS	-	GACCTGGCCG	GACCTGGCCG	rs139353034	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27040943_27040944insGACCTGGCCG								HS3ST4 (891935 upstream) : C16orf82 (37275 downstream)																							CAGTGGGTAATGACCAACCCCG	0.228													4	3	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	27957977	27957977	+	Intron	DEL	A	-	-	rs71140930		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27957977delA	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						agaaagaaagaaaagaaagaa	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	30534519	30534519	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30534519delT								ITGAL (14 upstream) : ZNF768 (804 downstream)																							TTTGTGGTGGTTTTGTGCTGG	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32494367	32494368	+	IGR	INS	-	T	T	rs143786075	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32494367_32494368insT								HERC2P4 (330493 upstream) : TP53TG3B (190473 downstream)																							ttaaacccttcttttcattcag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32528450	32528451	+	IGR	INS	-	C	C	rs113672595		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32528450_32528451insC								HERC2P4 (364576 upstream) : TP53TG3B (156390 downstream)																							acatcacaaagcatttctcaga	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33569704	33569704	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33569704delG								SLC6A10P (673241 upstream) : MIR1826 (395804 downstream)																							GGCTCCTCCTGGCCGACCCCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33981406	33981407	+	IGR	INS	-	G	G	rs145492969		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33981406_33981407insG								MIR1826 (15814 upstream) : UBE2MP1 (422395 downstream)																							aattcaacaaccttcatgctaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34492249	34492249	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34492249delA								UBE2MP1 (87487 upstream) : LOC283914 (105538 downstream)																							tgtggaatctaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34837674	34837675	+	IGR	INS	-	T	T	rs9673814		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34837674_34837675insT								LOC146481 (122707 upstream) : None (None downstream)																							ttctttttctgttttttttttt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46471263	46471263	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46471263delC								None (None upstream) : ANKRD26P1 (31986 downstream)																							caccttcttgctttctttcct	0.020													4	2	---	---	---	---	
ABCC11	85320	broad.mit.edu	37	16	48215179	48215180	+	Intron	DEL	AG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48215179_48215180delAG	uc002eff.1	-						ABCC11_uc002efg.1_Intron|ABCC11_uc002efh.1_Intron|ABCC11_uc010cbg.1_Intron	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				TATGTGTATCAGAGAGAGAGAG	0.351									Cerumen_Type				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51236072	51236072	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51236072delT								SALL1 (50889 upstream) : None (None downstream)																							CTTCAGGGCCTTTTCCTTTTA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52182569	52182569	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52182569delT								SALL1 (997386 upstream) : TOX3 (289349 downstream)																							TTTAGCATAATTTCCCGAGGC	0.398													4	2	---	---	---	---	
RLTPR	146206	broad.mit.edu	37	16	67688044	67688044	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67688044delC	uc002etn.2	+						RLTPR_uc010vjr.1_Intron	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin											breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		CCCCATGATGCCCCCCAGGTA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71350387	71350387	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71350387delG								FTSJD1 (26874 upstream) : CALB2 (42239 downstream)																							cgcccaggctggagtgcagtg	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77778797	77778798	+	IGR	INS	-	A	A	rs139097166		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77778797_77778798insA								NUDT7 (2644 upstream) : VAT1L (43685 downstream)																							ctgtgtcaaagaaaaaaaaaaa	0.178													3	3	---	---	---	---	
HSBP1	3281	broad.mit.edu	37	16	83843061	83843062	+	Intron	DEL	TC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83843061_83843062delTC	uc002fgy.1	+							NM_001537	NP_001528	O75506	HSBP1_HUMAN	heat shock factor binding protein 1						negative regulation of transcription from RNA polymerase II promoter	nucleus	transcription corepressor activity				0		all_cancers(2;0.00573)|all_epithelial(2;0.0309)		BRCA - Breast invasive adenocarcinoma(80;0.0404)		ttttttcttttcttttcttttt	0.213													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88514350	88514351	+	IGR	INS	-	A	A	rs55886266		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88514350_88514351insA								ZNF469 (7185 upstream) : ZFPM1 (5663 downstream)																							actcctgtctcaaaaaaaaaaa	0.010													4	3	---	---	---	---	
TRPV1	7442	broad.mit.edu	37	17	3477916	3477916	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3477916delG	uc010vrr.1	-						TRPV1_uc010vro.1_Intron|TRPV1_uc010vrp.1_Intron|TRPV1_uc010vrq.1_Intron|TRPV1_uc010vrs.1_Intron|TRPV1_uc010vrt.1_Intron|TRPV1_uc010vru.1_Intron	NM_080706	NP_542437	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel,						cell surface receptor linked signaling pathway|chemosensory behavior|thermoception	cell junction|dendritic spine membrane|integral to plasma membrane|postsynaptic membrane	ATP binding|calcium channel activity|calmodulin binding			ovary(1)	1				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	TGTGGGACTCGGATGAGCATC	0.363													4	2	---	---	---	---	
MYH3	4621	broad.mit.edu	37	17	10547483	10547486	+	Intron	DEL	AAAC	-	-	rs147605554		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10547483_10547486delAAAC	uc002gmq.1	-							NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,						muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						caaaaaaaaaaaacaaacaaaaaa	0.201													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20879789	20879789	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20879789delC	uc002gyk.1	+											Homo sapiens hypothetical protein LOC339260, mRNA (cDNA clone IMAGE:5168338), partial cds.																		GCTGACGTCTCCCCCCAACCC	0.493													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21196637	21196637	+	Intron	DEL	T	-	-	rs68015508		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21196637delT	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		TCCTTCCCTCTCCAGCGAGGC	0.657													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21328762	21328764	+	IGR	DEL	AGG	-	-	rs146874931		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21328762_21328764delAGG								KCNJ12 (5583 upstream) : C17orf51 (102808 downstream)																							gcagggagaaaggaggatattga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21345392	21345392	+	IGR	DEL	G	-	-	rs112741354		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21345392delG								KCNJ12 (22213 upstream) : C17orf51 (86180 downstream)																							GGGGAGGGCTGGGGGGGCAAG	0.502													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21514558	21514558	+	IGR	DEL	T	-	-	rs11328023		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21514558delT								C17orf51 (36827 upstream) : FAM27L (310812 downstream)																							attaaaaaaatctaccccaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21530245	21530246	+	IGR	INS	-	T	T	rs112632430	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21530245_21530246insT								C17orf51 (52514 upstream) : FAM27L (295124 downstream)																							tgtccggctaatttttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25296183	25296183	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25296183delC								None (None upstream) : WSB1 (324923 downstream)																							ctttcttgaacagtctatcca	0.045													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25668272	25668272	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25668272delC								WSB1 (27627 upstream) : KSR1 (130764 downstream)																							CTCTTCCCAGCCCCTGCAAGA	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48032052	48032053	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48032052_48032053insT								TAC4 (106673 upstream) : DLX4 (14509 downstream)																							ttctttctttctttttttttgg	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51556566	51556567	+	IGR	INS	-	A	A	rs149375608	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51556566_51556567insA								None (None upstream) : KIF2B (343672 downstream)																							CCCTTTACCCCGTAATTTTCAT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55841828	55841829	+	IGR	INS	-	TTGT	TTGT	rs139326965	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55841828_55841829insTTGT								MSI2 (84529 upstream) : MRPS23 (75015 downstream)																							agaggtagtaattgtttgtttg	0.079													3	4	---	---	---	---	
TRIM37	4591	broad.mit.edu	37	17	57129095	57129096	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57129095_57129096insT	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207	O94972	TRI37_HUMAN	tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AAAATACAAAGttttttttttt	0.208									Mulibrey_Nanism				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	59523151	59523152	+	IGR	INS	-	T	T	rs139821581	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59523151_59523152insT								C17orf82 (32510 upstream) : TBX4 (6627 downstream)																							ccTAATTTGCCTTTTTTTGTCC	0.238													0	7	---	---	---	---	
BRIP1	83990	broad.mit.edu	37	17	59770877	59770878	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59770877_59770878insA	uc002izk.1	-						BRIP1_uc002izl.1_Intron	NM_032043	NP_114432	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1						AATACATCTAGAAAAAATAGGG	0.337			F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				43	40	---	---	---	---	
EFCAB3	146779	broad.mit.edu	37	17	60475815	60475815	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60475815delA	uc002izu.1	+						EFCAB3_uc010wpc.1_Intron	NM_173503	NP_775774	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3 isoform b								calcium ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			acttagtctcaaaaaaaaaag	0.030													4	2	---	---	---	---	
TEX2	55852	broad.mit.edu	37	17	62301970	62301971	+	Intron	INS	-	C	C	rs149301054	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62301970_62301971insC	uc002jec.2	-						TEX2_uc002jed.2_Intron|TEX2_uc002jee.2_Intron	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2						signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		AGGTTCCCAGGCCCCTACTCAC	0.475													2	5	---	---	---	---	
CACNG4	27092	broad.mit.edu	37	17	65013614	65013615	+	Intron	INS	-	GTT	GTT	rs141518312	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65013614_65013615insGTT	uc002jft.1	+							NM_014405	NP_055220	Q9UBN1	CCG4_HUMAN	voltage-dependent calcium channel gamma-4						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane	voltage-gated calcium channel activity			central_nervous_system(1)	1	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			TGGGCAAATTCgttgttgttgt	0.272													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69227201	69227202	+	IGR	DEL	AC	-	-	rs148385591	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69227201_69227202delAC								None (None upstream) : SOX9 (889959 downstream)																							TTTTATATATacacacacacac	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70620581	70620581	+	IGR	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70620581delG								SOX9 (498029 upstream) : SLC39A11 (21505 downstream)																							GGCATCCTTTGAGTCACATAC	0.443													4	2	---	---	---	---	
COG1	9382	broad.mit.edu	37	17	71186343	71186344	+	5'Flank	INS	-	AA	AA	rs150817370	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71186343_71186344insAA	uc002jjg.2	+						COG1_uc002jjh.2_5'Flank|COG1_uc002jjf.1_5'Flank	NM_018714	NP_061184	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1						Golgi organization|intra-Golgi vesicle-mediated transport|protein transport	Golgi membrane|Golgi transport complex	protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.197)			AGAacacacacacacacacaca	0.292													5	4	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71563572	71563573	+	Intron	INS	-	GT	GT	rs140719137	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71563572_71563573insGT	uc010dfm.2	-							NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						ctgctagggcagtgtcaagcaa	0.000													0	7	---	---	---	---	
TTYH2	94015	broad.mit.edu	37	17	72243996	72243997	+	Intron	DEL	GT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72243996_72243997delGT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron|TTYH2_uc002jkd.2_5'Flank	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						gcgtgcatgcgtgtgtgtgtgt	0.332													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76539197	76539201	+	IGR	DEL	GTTTT	-	-	rs67935348		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76539197_76539201delGTTTT								DNAH17 (70341 upstream) : CYTH1 (130930 downstream)																							AAGATCATAGgttttgttttgtttt	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76987547	76987547	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76987547delC								LGALS3BP (11486 upstream) : CANT1 (252 downstream)																							aggtcatttgcctaaggacat	0.060													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77240786	77240787	+	Intron	INS	-	TC	TC	rs67580640		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77240786_77240787insTC	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			GAGccttcccttcccttccctt	0.238													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77373485	77373488	+	Intron	DEL	ACAC	-	-	rs79774406		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77373485_77373488delACAC	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			acacactcatacacacacagacat	0.142													1	5	---	---	---	---	
SGSH	6448	broad.mit.edu	37	17	78187722	78187723	+	Intron	DEL	AG	-	-	rs34029730		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78187722_78187723delAG	uc002jxz.3	-						SGSH_uc002jya.3_Intron|SGSH_uc002jxy.2_3'UTR|SGSH_uc010wue.1_Intron	NM_000199	NP_000190	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase precursor						proteoglycan metabolic process	lysosome	metal ion binding|N-sulfoglucosamine sulfohydrolase activity|sulfuric ester hydrolase activity			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TAGAACAGACAGACCGGGGGAG	0.663													3	9	---	---	---	---	
SLC26A11	284129	broad.mit.edu	37	17	78195120	78195121	+	Intron	INS	-	G	G	rs150002675	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78195120_78195121insG	uc002jyb.1	+						SGSH_uc002jxz.3_5'Flank|SGSH_uc002jya.3_5'Flank|SGSH_uc002jxy.2_5'Flank|SGSH_uc010wue.1_5'Flank|SLC26A11_uc002jyc.1_Intron|SLC26A11_uc002jyd.1_Intron|SLC26A11_uc010dhv.1_Intron	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			AGGATTTGCACGGGGGGGATTC	0.540													3	3	---	---	---	---	
C17orf55	284185	broad.mit.edu	37	17	79280765	79280765	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79280765delG	uc002kac.1	-							NM_178519	NP_848614			hypothetical protein LOC284185												0	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TGCCAGAGCCGGGGGCACAGC	0.642													4	2	---	---	---	---	
SECTM1	6398	broad.mit.edu	37	17	80281846	80281851	+	Intron	DEL	TGGGAG	-	-	rs113199635		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80281846_80281851delTGGGAG	uc002keo.2	-						SECTM1_uc002ken.2_Intron|SECTM1_uc002kep.2_Intron	NM_003004	NP_002995	Q8WVN6	SCTM1_HUMAN	secreted and transmembrane 1 precursor						immune response|mesoderm development|positive regulation of I-kappaB kinase/NF-kappaB cascade	extracellular space|Golgi apparatus|integral to membrane|plasma membrane	cytokine activity|signal transducer activity				0	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			GTGGACAACATGGGAGTGGGAGTGGG	0.670													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	107576	107577	+	5'Flank	INS	-	G	G			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:107576_107577insG	uc002kke.2	+											Homo sapiens Rho-associated, coiled-coil containing protein kinase 1, mRNA (cDNA clone IMAGE:5269982), complete cds.																		ctctgcctatagggggccttgt	0.000													5	3	---	---	---	---	
ENOSF1	55556	broad.mit.edu	37	18	679562	679562	+	Intron	DEL	A	-	-	rs35201185		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:679562delA	uc002kku.3	-						ENOSF1_uc002kkt.3_Intron|ENOSF1_uc010dke.2_Intron|ENOSF1_uc010dkf.2_Intron|ENOSF1_uc002kkv.3_Intron|ENOSF1_uc002kkw.3_Intron|ENOSF1_uc002kkx.3_Intron	NM_017512	NP_059982	Q7L5Y1	ENOF1_HUMAN	enolase superfamily 1 isoform rTS beta						cellular amino acid catabolic process	mitochondrion	isomerase activity|metal ion binding			ovary(1)	1						AAAATCCATGAAAAAAAAAAA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	874674	874675	+	IGR	DEL	AA	-	-	rs151116161		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:874674_874675delAA								YES1 (62132 upstream) : ADCYAP1 (30269 downstream)																							gtccattcataagtcttgagtt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	1200196	1200197	+	IGR	INS	-	AATA	AATA	rs141324054	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1200196_1200197insAATA								ADCYAP1 (288025 upstream) : C18orf2 (54193 downstream)																							tagctgcgcctaatacaggagg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2167027	2167027	+	IGR	DEL	T	-	-	rs71365153		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2167027delT								C18orf2 (759846 upstream) : METTL4 (370498 downstream)																							ccctggaaggttgttggtttg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2619976	2619976	+	IGR	DEL	T	-	-	rs35375005		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2619976delT								NDC80 (3343 upstream) : SMCHD1 (35910 downstream)																							tctggcctaattttttttttt	0.000													4	2	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8198046	8198046	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8198046delG	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				CTCTGCCTCTGGAATTTTTAG	0.463													4	2	---	---	---	---	
RAB31	11031	broad.mit.edu	37	18	9836993	9836993	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9836993delA	uc002kog.2	+							NM_006868	NP_006859	Q13636	RAB31_HUMAN	RAB31, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			skin(1)	1						GGTGAAACACAAAGGGGAGAG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14251862	14251863	+	5'Flank	DEL	CA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14251862_14251863delCA	uc002ksy.1	+						uc010xah.1_5'Flank					DQ590589																		tatgtgcgcgcacacacacaca	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22399897	22399900	+	IGR	DEL	CTCC	-	-	rs62083843		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22399897_22399900delCTCC								HRH4 (339977 upstream) : ZNF521 (241988 downstream)																							ctctctttctctccctccctccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	24263142	24263143	+	IGR	DEL	GC	-	-	rs34042984		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24263142_24263143delGC								KCTD1 (42834 upstream) : LOC728606 (4442 downstream)																							TTCCACGACAGCTGATATTTTA	0.416													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	30135551	30135552	+	IGR	INS	-	A	A	rs149788208	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30135551_30135552insA								WBP11P1 (40955 upstream) : KLHL14 (117082 downstream)																							AGAGAAGCAGGAAAAAAAAGCC	0.366													4	2	---	---	---	---	
NOL4	8715	broad.mit.edu	37	18	31726694	31726695	+	Intron	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31726694_31726695insT	uc010dmi.2	-						NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3						atttaaagtagttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35416391	35416391	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35416391delA								CELF4 (270391 upstream) : None (None downstream)																							tcagagggccaaaaactctac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37598876	37598877	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37598876_37598877insT								LOC647946 (218594 upstream) : None (None downstream)																							ACAACAACAACTTTTTTTAAGA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	40162800	40162800	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40162800delG	uc002lau.2	+											Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		ATGTAGATGAGGAAAAGTGAG	0.323													4	2	---	---	---	---	
RNF165	494470	broad.mit.edu	37	18	43977630	43977631	+	Intron	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43977630_43977631delTG	uc002lcb.1	+						RNF165_uc002lby.1_Intron|RNF165_uc010dnn.1_Intron	NM_152470	NP_689683	Q6ZSG1	RN165_HUMAN	ring finger protein 165								zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)		GGGGCAGAATtgtgtgtgtgtg	0.059													4	2	---	---	---	---	
WDR7	23335	broad.mit.edu	37	18	54616360	54616361	+	Intron	DEL	TC	-	-	rs112797585		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54616360_54616361delTC	uc002lgk.1	+						WDR7_uc002lgl.1_Intron	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		TTTTCTAAAGtctctctctctc	0.302													4	2	---	---	---	---	
ALPK2	115701	broad.mit.edu	37	18	56165670	56165670	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56165670delC	uc002lhj.3	-							NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						TAAGCAATCTCCCCAGAAATA	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57048239	57048239	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57048239delA								LMAN1 (21731 upstream) : CCBE1 (52910 downstream)																							TGGTAACCTGAAAAACAAAGA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57549674	57549674	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57549674delA								CCBE1 (185030 upstream) : PMAIP1 (17518 downstream)																							CGTGAGGTGGAAAAAAAAAAG	0.443													4	2	---	---	---	---	
PIGN	23556	broad.mit.edu	37	18	59748537	59748537	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59748537delA	uc002lii.3	-						PIGN_uc002lij.3_Intron	NM_176787	NP_789744	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)				GTATGGCAGTAAGGGTGGCTG	0.358													4	2	---	---	---	---	
PIGN	23556	broad.mit.edu	37	18	59754125	59754127	+	Intron	DEL	ACA	-	-	rs146234255		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59754125_59754127delACA	uc002lii.3	-						PIGN_uc002lij.3_Intron	NM_176787	NP_789744	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)				gttaaatatgacaacaagttgga	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	60771140	60771141	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60771140_60771141insT								PHLPP1 (123475 upstream) : BCL2 (19438 downstream)																							gttgtgctgtggtgtgatgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62045075	62045076	+	Intron	INS	-	A	A	rs35220685		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62045075_62045076insA	uc002ljx.2	+											Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																		GGACATTTGAGAAAAAAAAAAA	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62457933	62457934	+	IGR	DEL	TC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62457933_62457934delTC								C18orf20 (641673 upstream) : CDH7 (959554 downstream)																							GTAATTAGGAtctctctctctc	0.238													4	2	---	---	---	---	
FAM69C	125704	broad.mit.edu	37	18	72109566	72109566	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72109566delT	uc002llk.2	-							NM_001044369	NP_001037834	Q0P6D2	FA69C_HUMAN	hypothetical protein LOC125704							endoplasmic reticulum membrane|integral to membrane					0						tttctttttcttttttttttt	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73978287	73978299	+	IGR	DEL	AGGAAGGAAGGAA	-	-	rs138141195	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73978287_73978299delAGGAAGGAAGGAA								C18orf62 (838698 upstream) : ZNF516 (93320 downstream)																							gaagggagggaggaaggaaggaaaggaaggaag	0.000													4	2	---	---	---	---	
FSD1	79187	broad.mit.edu	37	19	4315731	4315731	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4315731delC	uc002lzy.2	+						FSD1_uc002lzz.2_Intron|FSD1_uc002maa.2_Intron	NM_024333	NP_077309	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing						cell division|mitosis	cleavage furrow|microtubule|microtubule organizing center|nucleus				skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		gccccagcctccccagtagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5372738	5372739	+	IGR	INS	-	TC	TC	rs146503434	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5372738_5372739insTC								PTPRS (31924 upstream) : ZNRF4 (82687 downstream)																							GTGCACACATGTCTGTGAGCAC	0.168													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8865564	8865565	+	IGR	INS	-	A	A	rs148286254		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8865564_8865565insA								OR2Z1 (23230 upstream) : ZNF558 (54817 downstream)																							atcaaaaaattaaaaaaaaaaa	0.238													4	2	---	---	---	---	
ZNF560	147741	broad.mit.edu	37	19	9586216	9586216	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9586216delA	uc002mlp.1	-						ZNF560_uc010dwr.1_Intron	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6						CTAGAGCAAGAAAAAGGAATT	0.294													4	2	---	---	---	---	
LDLR	3949	broad.mit.edu	37	19	11233654	11233654	+	Intron	DEL	T	-	-	rs35951147		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11233654delT	uc002mqk.3	+						LDLR_uc010xlk.1_Intron|LDLR_uc010xll.1_Intron|LDLR_uc010xlm.1_Intron|LDLR_uc010xln.1_Intron|LDLR_uc010xlo.1_Intron	NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor						cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)|skin(2)	4		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	acctggctaattttttttttt	0.000													3	3	---	---	---	---	
MAN2B1	4125	broad.mit.edu	37	19	12761172	12761172	+	Intron	DEL	T	-	-	rs35532533		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12761172delT	uc002mub.2	-						MAN2B1_uc010dyv.1_Intron	NM_000528	NP_000519	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1						protein deglycosylation	lysosome	alpha-mannosidase activity|zinc ion binding			ovary(4)|central_nervous_system(2)	6						CACATAAttcttttttttttt	0.249													4	2	---	---	---	---	
MED26	9441	broad.mit.edu	37	19	16739514	16739515	+	5'Flank	INS	-	C	C	rs11396283		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16739514_16739515insC	uc002nen.1	-						MED26_uc002nee.2_5'Flank	NM_004831	NP_004822	O95402	MED26_HUMAN	mediator complex subunit 26						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|RNA polymerase II transcription cofactor activity|transcription coactivator activity			ovary(2)	2						TGTCGCCGCGGCCCCCCCGCCC	0.678													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21768194	21768195	+	Intron	INS	-	T	T	rs149308036	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21768194_21768195insT	uc002nqe.2	-						uc002nqf.1_5'Flank					full-length cDNA clone CS0DH004YH18 of T cells (Jurkat cell line) of Homo sapiens (human).																		ACAGATGTGGGAACCCCACCTC	0.530													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24582975	24582976	+	IGR	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24582975_24582976insA								LOC100101266 (236726 upstream) : None (None downstream)																							attcaactctcagtgttgaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27865506	27865507	+	IGR	DEL	TC	-	-	rs71224979		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27865506_27865507delTC								None (None upstream) : LOC148189 (415895 downstream)																							gttgaacgtatcttttTTTTTt	0.000													7	4	---	---	---	---	
CHST8	64377	broad.mit.edu	37	19	34234165	34234165	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34234165delT	uc002nus.3	+						CHST8_uc002nut.3_Intron|CHST8_uc002nuu.2_Intron	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)						carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)					tttgggagccttttgatctct	0.000													4	2	---	---	---	---	
HPN	3249	broad.mit.edu	37	19	35546654	35546655	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35546654_35546655insA	uc002nxq.1	+						HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_Intron|HPN_uc002nxt.1_Intron	NM_002151	NP_002142	P05981	HEPS_HUMAN	hepsin						cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	ACAAAGGGGATATGACTCACTC	0.287													4	2	---	---	---	---	
LGI4	163175	broad.mit.edu	37	19	35622689	35622689	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35622689delT	uc002nxx.2	-						LGI4_uc002nxy.1_Intron|LGI4_uc002nxz.1_Intron|LGI4_uc002nya.2_Intron	NM_139284	NP_644813	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4							extracellular region				pancreas(1)	1	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CCCATGAGCCTCACACATGAG	0.597													4	2	---	---	---	---	
DPF1	8193	broad.mit.edu	37	19	38717658	38717677	+	5'Flank	DEL	CTTCCTTCCTTCCTTCCTTT	-	-	rs71179424		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38717658_38717677delCTTCCTTCCTTCCTTCCTTT	uc002ohl.2	-						DPF1_uc002ohm.2_5'Flank|DPF1_uc002ohn.2_Intron|DPF1_uc010xtu.1_Intron|DPF1_uc010xtv.1_Intron|DPF1_uc010xtw.1_Intron	NM_004647	NP_004638	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1 isoform						induction of apoptosis|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nBAF complex	zinc ion binding				0	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			tccttccttccttccttccttccttcctttctttctttct	0.091													3	3	---	---	---	---	
YIF1B	90522	broad.mit.edu	37	19	38801927	38801927	+	Intron	DEL	A	-	-	rs75929446		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38801927delA	uc002ohz.2	-						YIF1B_uc002ohw.2_5'Flank|YIF1B_uc002ohx.2_Intron|YIF1B_uc010xtx.1_Intron|YIF1B_uc010xty.1_Intron|YIF1B_uc002oia.2_Intron|YIF1B_uc002ohy.2_Intron|YIF1B_uc002oib.2_Intron	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5							integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			accctgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	39679670	39679671	+	IGR	INS	-	T	T	rs148912814	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39679670_39679671insT								PAK4 (9624 upstream) : NCCRP1 (7933 downstream)																							acctcaaggcctttgcactgac	0.005													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	39984917	39984917	+	IGR	DEL	T	-	-	rs74178081		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39984917delT								TIMM50 (3389 upstream) : DLL3 (4640 downstream)																							ATTTTTTGCATTTTTTTTTTT	0.055													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	44234328	44234330	+	IGR	DEL	GGG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44234328_44234330delGGG								IRGC (10161 upstream) : C19orf61 (971 downstream)																							GGCAGGGGGTGGGGGAGGGCAAT	0.547													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45214289	45214290	+	IGR	INS	-	A	A	rs146158913	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45214289_45214290insA								CEACAM16 (305 upstream) : BCL3 (37688 downstream)																							ttgtcacctggccccgaaacag	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45693614	45693615	+	IGR	INS	-	TC	TC	rs145776816	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45693614_45693615insTC								BLOC1S3 (8557 upstream) : EXOC3L2 (22264 downstream)																							agacccctccttctctctctct	0.000													5	4	---	---	---	---	
PPP5C	5536	broad.mit.edu	37	19	46851198	46851198	+	Intron	DEL	A	-	-	rs76708803		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46851198delA	uc002pem.2	+						PPP5C_uc010xya.1_Intron|PPP5C_uc002pen.2_Intron	NM_006247	NP_006238	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit						mitosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein dephosphorylation|transcription, DNA-dependent	Golgi apparatus|nucleus	metal ion binding|protein binding|protein serine/threonine phosphatase activity|signal transducer activity			lung(1)|pancreas(1)	2		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		accagacatgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GRLF1	2909	broad.mit.edu	37	19	47491093	47491094	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47491093_47491094insA	uc010ekv.2	+							NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		GAAGCATCTAGAAAAATCAAAC	0.436													4	2	---	---	---	---	
SLC8A2	6543	broad.mit.edu	37	19	47968537	47968537	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47968537delT	uc002pgx.2	-						SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Intron	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		GAATGGAGGATGTCTTATTGC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	48080439	48080440	+	IGR	INS	-	T	T			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48080439_48080440insT								ZNF541 (21326 upstream) : GLTSCR1 (31013 downstream)																							ttcttgttttcttttTTTTTTT	0.173													4	2	---	---	---	---	
CARD8	22900	broad.mit.edu	37	19	48728394	48728395	+	Intron	INS	-	ATAA	ATAA	rs139373507	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48728394_48728395insATAA	uc002pie.3	-						CARD8_uc002pii.3_Intron|CARD8_uc010xzi.1_Intron|CARD8_uc010els.2_Intron|CARD8_uc010xzj.1_Intron|CARD8_uc010xzk.1_Intron|CARD8_uc002pif.3_Intron|CARD8_uc002pig.3_Intron|CARD8_uc002pih.3_Intron|CARD8_uc010xzl.1_Intron|CARD8_uc010xzm.1_Intron	NM_014959	NP_055774	Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8						negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		AGAAGCAGATCATAAATAAATA	0.297													3	3	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50795773	50795773	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50795773delT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron|MYH14_uc010ycb.1_Intron|MYH14_uc002prs.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GATGTGAAGCTGGGGAGGTGG	0.657													4	4	---	---	---	---	
C19orf75	284369	broad.mit.edu	37	19	51767771	51767771	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51767771delA	uc002pwb.1	+						C19orf75_uc010eov.1_Intron|C19orf75_uc010ycw.1_Intron	NM_173635	NP_775906	Q8N7X8	CS075_HUMAN	hypothetical protein LOC284369							integral to membrane				ovary(1)|pancreas(1)	2						GACTCAGGTGAAGAGACCGAG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	52062969	52062972	+	IGR	DEL	CATC	-	-	rs144225113		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52062969_52062972delCATC								SIGLEC6 (27905 upstream) : ZNF175 (11559 downstream)																							atcattcattcatccatccatcca	0.162													3	3	---	---	---	---	
ZNF836	162962	broad.mit.edu	37	19	52666772	52666772	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52666772delA	uc010ydi.1	-						ZNF836_uc010ydj.1_Intron	NM_001102657	NP_001096127	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						tcacgcctgtaatcccagcac	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54637247	54637248	+	IGR	INS	-	CT	CT	rs141571907	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54637247_54637248insCT								PRPF31 (2097 upstream) : CNOT3 (4201 downstream)																							ctccacctcccctctctctccc	0.089													6	3	---	---	---	---	
MBOAT7	79143	broad.mit.edu	37	19	54690818	54690819	+	Intron	INS	-	C	C	rs143730615	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54690818_54690819insC	uc002qdq.2	-						MBOAT7_uc010erg.2_Intron|MBOAT7_uc010yem.1_Intron|MBOAT7_uc002qdr.2_Intron|MBOAT7_uc002qds.2_Intron|MBOAT7_uc010yen.1_Intron|MBOAT7_uc002qdt.3_Intron	NM_024298	NP_077274	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					ACCTACTGTTACCTATGTGGGT	0.327													4	3	---	---	---	---	
KIR3DX1	90011	broad.mit.edu	37	19	55053966	55053966	+	Intron	DEL	T	-	-	rs66488179		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55053966delT	uc010erm.2	+						KIR3DX1_uc010yfa.1_Intron|KIR3DX1_uc010yfb.1_Intron|KIR3DX1_uc010yfc.1_Intron|KIR3DX1_uc010yfd.1_Intron					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		GCTGAGGttcttttttttttt	0.294													6	4	---	---	---	---	
SSC5D	284297	broad.mit.edu	37	19	56029616	56029617	+	In_Frame_Ins	INS	-	CCA	CCA	rs150781976	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56029616_56029617insCCA	uc002qlg.3	+	14	4060_4061	c.3973_3974insCCA	c.(3973-3975)CCC>CCCACC	p.1327_1328insT		NM_001144950	NP_001138422	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine-rich glycoprotein	1327_1328	Thr-rich.|Pro-rich.					extracellular region|membrane	scavenger receptor activity				0						gacccctcaccccACAACTCCT	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	58676461	58676461	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58676461delC								ZNF329 (9984 upstream) : ZNF274 (17935 downstream)																							ccactgccctccagcctgggt	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	3419563	3419566	+	IGR	DEL	ACAC	-	-	rs35749569		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3419563_3419566delACAC								C20orf194 (30976 upstream) : ATRN (32099 downstream)																							caaaaTacatacacacacacacac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	5624262	5624263	+	IGR	INS	-	T	T	rs149864827	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5624262_5624263insT								GPCPD1 (32590 upstream) : C20orf196 (106780 downstream)																							tttttcttttctttttttttga	0.094													4	2	---	---	---	---	
C20orf103	24141	broad.mit.edu	37	20	9501606	9501607	+	Intron	INS	-	G	G	rs144595765	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9501606_9501607insG	uc002wni.1	+						C20orf103_uc010zrc.1_Intron	NM_012261	NP_036393	Q9UJQ1	CT103_HUMAN	chromosome 20 open reading frame 103 precursor							integral to membrane				upper_aerodigestive_tract(1)|lung(1)|breast(1)	3			COAD - Colon adenocarcinoma(9;0.194)			cacgcagagttggttcacttag	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	9938422	9938423	+	IGR	DEL	TC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9938422_9938423delTC								PAK7 (118735 upstream) : ANKRD5 (77274 downstream)																							tcctacatgatctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11082389	11082389	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11082389delT								JAG1 (427695 upstream) : BTBD3 (789088 downstream)																							ctcttttttgtttttttgaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16594393	16594393	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16594393delT								KIF16B (40315 upstream) : SNRPB2 (116236 downstream)																							CTGTGTGTCCTGAATTGCAAT	0.403													4	2	---	---	---	---	
DTD1	92675	broad.mit.edu	37	20	18680006	18680006	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18680006delA	uc002wrf.3	+							NM_080820	NP_543010	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2						CAGCAGTAGGAACAGAGAAGG	0.502													4	2	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20580780	20580781	+	Intron	INS	-	A	A			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20580780_20580781insA	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						ctctactgaagaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24195709	24195709	+	Intron	DEL	T	-	-	rs143859069		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24195709delT	uc002wtv.1	+											Homo sapiens cDNA FLJ33581 fis, clone BRAMY2011846.																		ggctgctcccttgtgaatgag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26082949	26082950	+	IGR	DEL	AT	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26082949_26082950delAT								FAM182A (15397 upstream) : C20orf191 (1103 downstream)																							taaacaaaacatagtatactca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29448107	29448109	+	IGR	DEL	GAA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29448107_29448109delGAA								None (None upstream) : FRG1B (163770 downstream)																							CAGCAAAAATGAAGAATAGATAT	0.266													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29465535	29465535	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29465535delT								None (None upstream) : FRG1B (146344 downstream)																							gggttgttagtttttttttcc	0.000													3	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29618862	29618863	+	Intron	DEL	CT	-	-	rs112384226		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29618862_29618863delCT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0						aggtctctacctctctctgtgt	0.000													3	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29646130	29646131	+	Intron	INS	-	T	T	rs147868553		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29646130_29646131insT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						ttaaaataaaatttaaaaaaTA	0.035													4	2	---	---	---	---	
FOXS1	2307	broad.mit.edu	37	20	30434246	30434247	+	5'Flank	DEL	AG	-	-	rs71899789		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30434246_30434247delAG	uc002wwt.1	-							NM_004118	NP_004109	O43638	FOXS1_HUMAN	forkhead box S1						anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|insulin receptor signaling pathway|lymphangiogenesis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|neural crest cell fate commitment|neuromuscular process controlling balance|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of multicellular organism growth|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|somitogenesis|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)	1						AGGAATGAATagagagagagag	0.406													4	2	---	---	---	---	
TTLL9	164395	broad.mit.edu	37	20	30521222	30521222	+	Intron	DEL	A	-	-	rs113180138		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30521222delA	uc010gdx.1	+						TTLL9_uc002wwy.1_Intron|TTLL9_uc002wwz.1_Intron|TTLL9_uc002wxa.1_Intron|TTLL9_uc002wxb.1_Intron|TTLL9_uc010zto.1_Intron|TTLL9_uc002wxc.2_Intron|TTLL9_uc010ztp.1_Intron|TTLL9_uc010ztq.1_Intron	NM_001008409	NP_001008409	Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9						protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity			ovary(2)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CTCTTGAATTAAAAAAAAAAA	0.184													4	3	---	---	---	---	
FAM83D	81610	broad.mit.edu	37	20	37578762	37578762	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37578762delC	uc002xjg.2	+							NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610						cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)				ccgtgcccagccAGATCCTGG	0.199													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37787455	37787455	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37787455delT								DHX35 (119092 upstream) : LOC339568 (54969 downstream)																							gcccagctaattttttttttt	0.000													4	2	---	---	---	---	
CHD6	84181	broad.mit.edu	37	20	40036869	40036869	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40036869delG	uc002xka.1	-						CHD6_uc002xjz.1_Intron	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				agctgggggtgggggtgggga	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40409304	40409304	+	IGR	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40409304delA								CHD6 (162171 upstream) : PTPRT (292089 downstream)																							ctctgcctggaaagatctctc	0.010													4	2	---	---	---	---	
TOX2	84969	broad.mit.edu	37	20	42546693	42546693	+	Intron	DEL	C	-	-	rs11479345		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42546693delC	uc010ggo.2	+						TOX2_uc002xle.3_Intron|TOX2_uc010ggp.2_Intron	NM_001098797	NP_001092267	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			aggtttgactcccagCAGGAC	0.209													4	4	---	---	---	---	
KCNK15	60598	broad.mit.edu	37	20	43374018	43374019	+	5'Flank	INS	-	GAAAG	GAAAG	rs150750005	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43374018_43374019insGAAAG	uc002xmr.2	+							NM_022358	NP_071753	Q9H427	KCNKF_HUMAN	potassium family, subfamily K, member 15							integral to membrane	potassium channel activity|voltage-gated ion channel activity				0		Myeloproliferative disorder(115;0.0122)				gaagaagagatgaagggacgaa	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44056080	44056081	+	IGR	INS	-	GTG	GTG	rs143824542	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44056080_44056081insGTG								PIGT (1196 upstream) : WFDC2 (42313 downstream)																							GGACTTAACACGTGTTCCTTAT	0.505													4	2	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45252047	45252047	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45252047delT	uc002xsf.1	-						SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron|SLC13A3_uc002xsi.3_Intron	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CCTCTCTAtctttttttgaac	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51461898	51461899	+	IGR	INS	-	TCCT	TCCT	rs112159104		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51461898_51461899insTCCT								ZFP64 (653374 upstream) : TSHZ2 (126978 downstream)																							tcctttcttcctccctccctcc	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52423679	52423679	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52423679delT								ZNF217 (212878 upstream) : SUMO1P1 (67363 downstream)																							ctccctctccttcattcaaca	0.000													4	2	---	---	---	---	
CASS4	57091	broad.mit.edu	37	20	54994330	54994330	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54994330delT	uc002xxp.2	+						CASS4_uc002xxq.3_Intron|CASS4_uc002xxr.2_Intron|CASS4_uc010zze.1_Intron|CASS4_uc010gio.2_Intron	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a						cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3						AGGAAATACATTTTTTAGGAA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55991174	55991175	+	IGR	INS	-	GA	GA	rs74182720		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55991174_55991175insGA								RBM38 (6790 upstream) : CTCFL (72705 downstream)																							TGTCTGATCCTGAGAGAGAGAG	0.361													6	4	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59838020	59838021	+	Intron	INS	-	GA	GA	rs147489175	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59838020_59838021insGA	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			AATCATGAACTgagagagagag	0.228													3	3	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59858001	59858001	+	Intron	DEL	G	-	-	rs67326049		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59858001delG	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			cgtgtgctgtggcgtgtgatg	0.000													3	5	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60101227	60101227	+	Intron	DEL	T	-	-	rs2149480		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60101227delT	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CTGGTGCCCCTCCCCCTCCCC	0.587													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61079452	61079460	+	IGR	DEL	TCCATCATC	-	-	rs62196344		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61079452_61079460delTCCATCATC								GATA5 (28426 upstream) : C20orf200 (62095 downstream)																							caccatcatttccatcatcaccatcacca	0.033													3	5	---	---	---	---	
TCEA2	6919	broad.mit.edu	37	20	62698557	62698557	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62698557delC	uc011abs.1	+						TCEA2_uc011abr.1_Intron|TCEA2_uc010gkq.2_Intron|TCEA2_uc010gks.2_Intron|TCEA2_uc010gkt.2_Intron|TCEA2_uc010gku.1_Intron	NM_003195	NP_003186	Q15560	TCEA2_HUMAN	transcription elongation factor A protein 2						regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	transcription elongation factor complex	DNA binding|protein binding|translation elongation factor activity|zinc ion binding				0	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					TCAGTGGGTGCCTGTCAGCAT	0.632													4	2	---	---	---	---	
MYT1	4661	broad.mit.edu	37	20	62811411	62811414	+	Intron	DEL	ACAC	-	-	rs139161620		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62811411_62811414delACAC	uc002yii.2	+						MYT1_uc002yih.2_Intron	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1						cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					acacacagttacacaccacacgca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9668184	9668186	+	IGR	DEL	TTC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9668184_9668186delTTC								None (None upstream) : None (None downstream)																							tttcttttctttctttttTCTAC	0.212													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10441381	10441382	+	IGR	DEL	AA	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10441381_10441382delAA								None (None upstream) : TPTE (465361 downstream)																							actctgtctcaaaaaaaaaaaa	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10834671	10834672	+	IGR	INS	-	AATGG	AATGG	rs145794084		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10834671_10834672insAATGG								None (None upstream) : TPTE (72071 downstream)																							ggaatggtcccaatggaatgga	0.000													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10984603	10984605	+	Intron	DEL	CTC	-	-	rs71277400		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10984603_10984605delCTC	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATCTTTGCTTCTCCTCAAATAGG	0.458													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10993858	10993861	+	5'Flank	DEL	TTTG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10993858_10993861delTTTG	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_5'Flank|TPTE_uc002yir.1_5'Flank|TPTE_uc010gkv.1_5'Flank	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCCTTGGGTTtttgtttgtttgtt	0.225													1	6	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11031726	11031726	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11031726delA	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aacctgctacaagagtctact	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11041957	11041963	+	Intron	DEL	AGTTTTG	-	-	rs67727472		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11041957_11041963delAGTTTTG	uc002yit.1	-						TPTE_uc002yis.1_5'Flank	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AATTTCATATAGTTTTGAGTTTTGAAA	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11112605	11112606	+	IGR	DEL	AT	-	-	rs141194664		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11112605_11112606delAT								BAGE (13668 upstream) : None (None downstream)																							CTATTCTACCATATGTGTTGAA	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14368309	14368310	+	IGR	INS	-	AG	AG	rs150284364		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14368309_14368310insAG								None (None upstream) : C21orf99 (42177 downstream)																							atactgcaaaaagtgtttcaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18570199	18570200	+	IGR	INS	-	AGGA	AGGA	rs149741218	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18570199_18570200insAGGA								C21orf34 (588105 upstream) : CXADR (315130 downstream)																							ggaaggaagggaggaaggaagg	0.104													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	19962076	19962077	+	Intron	INS	-	TCTGGTC	TCTGGTC	rs138092259	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19962076_19962077insTCTGGTC	uc010glf.1	-						uc002ykx.2_Intron					Homo sapiens, clone IMAGE:5392784, mRNA.																		ttttcccaataacccccttttt	0.000													4	2	---	---	---	---	
NCAM2	4685	broad.mit.edu	37	21	22645255	22645256	+	Intron	DEL	CA	-	-	rs67208865		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22645255_22645256delCA	uc002yld.1	+						NCAM2_uc011acb.1_Intron|NCAM2_uc011acc.1_Intron	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GACATGCATTcacacacacaca	0.168													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	23046776	23046776	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23046776delC								NCAM2 (135562 upstream) : None (None downstream)																							actctttcatccacatcactc	0.000													4	2	---	---	---	---	
HUNK	30811	broad.mit.edu	37	21	33360959	33360960	+	Intron	DEL	TC	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33360959_33360960delTC	uc002yph.2	+							NM_014586	NP_055401	P57058	HUNK_HUMAN	hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2						CCCTCATttttctctcttttct	0.054													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35597030	35597031	+	IGR	DEL	AA	-	-	rs78780393		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35597030_35597031delAA								C21orf82 (34810 upstream) : KCNE2 (139292 downstream)																							agaccctgccaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37577246	37577246	+	Intron	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37577246delC	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						agccactgcacccagcACCAA	0.214													4	2	---	---	---	---	
HLCS	3141	broad.mit.edu	37	21	38156124	38156125	+	Intron	DEL	AC	-	-	rs71328509		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38156124_38156125delAC	uc010gnb.2	-						HLCS_uc002yvs.2_Intron	NM_000411	NP_000402	P50747	BPL1_HUMAN	holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	acatgcacatacacacacacac	0.351													4	2	---	---	---	---	
ETS2	2114	broad.mit.edu	37	21	40187100	40187113	+	Intron	DEL	GTGTGTGTGTGTGT	-	-	rs5843932		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40187100_40187113delGTGTGTGTGTGTGT	uc002yxg.2	+						ETS2_uc002yxf.2_Intron	NM_005239	NP_005230	P15036	ETS2_HUMAN	v-ets erythroblastosis virus E26 oncogene						positive regulation of transcription, DNA-dependent|skeletal system development	nucleus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)|pancreas(1)	4		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				CTTTAtgtgagtgtgtgtgtgtgtgtgtgtgtgt	0.336													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44757178	44757179	+	IGR	INS	-	TCT	TCT			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44757178_44757179insTCT								CRYAA (164265 upstream) : SIK1 (77219 downstream)																							caccaacaccaccaccaccacc	0.000													6	3	---	---	---	---	
CECR1	51816	broad.mit.edu	37	22	17681772	17681773	+	Intron	INS	-	A	A	rs35787601		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17681772_17681773insA	uc002zmk.1	-						CECR1_uc010gqu.1_Intron|CECR1_uc011agi.1_Intron|CECR1_uc011agj.1_Intron|CECR1_uc002zmj.1_5'Flank	NM_017424	NP_059120	Q9NZK5	CECR1_HUMAN	cat eye syndrome critical region protein 1						adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				aactctgcctcaaaaaaaaaaa	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17766518	17766518	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17766518delC								CECR1 (63780 upstream) : CECR2 (74321 downstream)																							TGTTTCACCGCCCCCCCACCA	0.333													4	2	---	---	---	---	
TUBA8	51807	broad.mit.edu	37	22	18581974	18581974	+	Intron	DEL	A	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18581974delA	uc002znr.2	+							NM_018943	NP_061816	Q9NY65	TBA8_HUMAN	tubulin, alpha 8						microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0						CAGCCCAGGGAAAAAGGTGCA	0.433													4	2	---	---	---	---	
PI4KA	5297	broad.mit.edu	37	22	21176675	21176676	+	Intron	DEL	CA	-	-	rs10610918		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21176675_21176676delCA	uc002zsz.3	-						PI4KA_uc010gsq.1_Intron	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			tcttctttcgcacctgcttctc	0.020													2	4	---	---	---	---	
BCR	613	broad.mit.edu	37	22	23608269	23608269	+	Intron	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23608269delT	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.1_Intron	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12						tgaccttgacttttttttttt	0.000			T	ABL1| FGFR1|JAK2 	CML|ALL|AML								4	2	---	---	---	---	
SGSM1	129049	broad.mit.edu	37	22	25206309	25206309	+	Intron	DEL	T	-	-	rs113798807		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25206309delT	uc003abg.2	+						SGSM1_uc003abh.2_Intron|SGSM1_uc010guu.1_Intron|SGSM1_uc003abj.2_Intron|SGSM1_uc003abf.2_Intron	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1							Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5						GCAAGCATCCTTTTTTTTTTT	0.478													4	3	---	---	---	---	
NF2	4771	broad.mit.edu	37	22	30073573	30073574	+	Intron	DEL	GG	-	-	rs35161712		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30073573_30073574delGG	uc003age.3	+						NF2_uc003afy.3_Intron|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Intron|NF2_uc003agb.3_Intron|NF2_uc003agc.3_Intron|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Intron|NF2_uc003aga.3_Intron|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Intron|NF2_uc010gvp.2_Intron|NF2_uc011akq.1_Intron	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						GTGGGCCGGTGGGGAGCCCTTT	0.594			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	31716780	31716780	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31716780delT								PIK3IP1 (28260 upstream) : PATZ1 (5011 downstream)																							AGAAGGGACCttttttttttt	0.045													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33751865	33751865	+	Intron	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33751865delG	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				TGTCCTACCAGGCATTCTGTA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47717228	47717228	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47717228delT								TBC1D22A (147506 upstream) : None (None downstream)																							cactgaactcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49537385	49537386	+	IGR	INS	-	A	A	rs149485532	by1000genomes	TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49537385_49537386insA								FAM19A5 (389643 upstream) : C22orf34 (270790 downstream)																							GATAAAACCCTAAACCCCTGTC	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	724197	724197	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:724197delT								SHOX (104052 upstream) : CRLF2 (590690 downstream)																							ccattgaaccttttttttttt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	48305869	48305869	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48305869delT								SSX4 (53084 upstream) : SLC38A5 (11059 downstream)																							ATAATACCCATTTTTTTTCTG	0.353													4	3	---	---	---	---	
STARD8	9754	broad.mit.edu	37	X	67937289	67937289	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67937289delC	uc004dxa.2	+	5	665	c.293delC	c.(292-294)GCCfs	p.A98fs	STARD8_uc004dxb.2_Frame_Shift_Del_p.A178fs|STARD8_uc004dxc.3_Frame_Shift_Del_p.A98fs	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	98					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6						CCAGGCCGTGCCCCCAGCTCG	0.647													4	5	---	---	---	---	
GRIA3	2892	broad.mit.edu	37	X	122460221	122460221	+	Intron	DEL	A	-	-	rs146181168		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122460221delA	uc004etq.3	+						GRIA3_uc004etr.3_Intron|GRIA3_uc004ets.3_Intron|GRIA3_uc011muf.1_Intron	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)	GTGGCTGCAGaaaaaaaaaaa	0.308													3	3	---	---	---	---	
GPR101	83550	broad.mit.edu	37	X	136113576	136113576	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136113576delG	uc011mwh.1	-	1	258	c.258delC	c.(256-258)CCCfs	p.P86fs		NM_054021	NP_473362	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	86	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					CCACCACCCAGGGGGCCACGA	0.617													17	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9933184	9933184	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9933184delT								TTTY22 (282330 upstream) : None (None downstream)																							ccatcttgagttgattttggt	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9951061	9951061	+	IGR	DEL	C	-	-	rs138842383		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9951061delC								TTTY22 (300207 upstream) : None (None downstream)																							ctgtgacctaccaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9981809	9981809	+	IGR	DEL	C	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9981809delC								TTTY22 (330955 upstream) : None (None downstream)																							TGATCTCAGACCAAAATATAG	0.408													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10014853	10014853	+	IGR	DEL	T	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10014853delT								TTTY22 (363999 upstream) : None (None downstream)																							ggggtttcactctgtcaccca	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10019370	10019371	+	IGR	INS	-	CC	CC	rs147406097		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10019370_10019371insCC								TTTY22 (368516 upstream) : None (None downstream)																							cacactgaacacccccgtcaga	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10072069	10072070	+	IGR	DEL	AG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10072069_10072070delAG								TTTY22 (421215 upstream) : None (None downstream)																							ttctacaaaaagagtgtctcga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13262505	13262506	+	IGR	DEL	TG	-	-			TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13262505_13262506delTG								None (None upstream) : None (None downstream)																							atttattttctgtgtcattgtt	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59014683	59014684	+	IGR	DEL	AT	-	-	rs10534960		TCGA-66-2789-01A-01D-0983-08	TCGA-66-2789-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59014683_59014684delAT								None (None upstream) : None (None downstream)																							acaaaacagaatgagagttccc	0.035													4	2	---	---	---	---	
